Counterintuitively,
Avoid Weapon Special Abilities that Inflict Damage
If your PC has been taking feats like Favored in House (ECS 53), and Least Dragonmark (mark of finding (ECS 64)) (ECS 53), and Skill Focus (Bluff) (PH 100) so he can better make Seduce to Learn Secret checks while the other PCs have been specializing in monster murdering, and they realize you aren't contributing much in a fight, explain that you'll need their help. As a swashbuckler (who doesn't cast spells) you were going to need it anyway. That's not an insult but a fact of mid- and high-level play.
You'll need their help because the first weapon special ability you add to your rapier is spell storing (DMG 225) (+1 bonus). No other weapon special ability scales for damage as well as it does because it scales with your party, one of whom should be happy to refill your +1 spell storing rapier free of charge at the end of a slow adventuring day. If you must fill your own tank, take ranks in the Use Magic Device skill and load your +1 spell storing rapier using a wand of combust [evoc] (SpC 50) (2nd-level spell at caster level 10) (300 gp/charge) or a wand of vampiric touch [necro] (PH 298) (3rd-level spell at caster level 20) (900 gp/charge) or a wand of another spell that the Comments will inevitably suggest.
It sounds like you're in a game wherein sources of magic items are restricted. If you aren't, also consider the weapon special ability bloodstone (MIC 29) (+1 bonus), which is like the weapon special ability spell storing that only holds the spell vampiric touch but the touch is modified by the feat Empower Spell (PH 93) for free. Seriously. Then add the weapon special ability power storing (MIC 40) (+1 bonus) if there's a psion available; my unfamiliarity with psionics means I don't know what's best, but there must be something awesome and Eberron is psionics-friendly. Then virtually guarantee your attack hits by adding the weapon special ability impaling (MIC 37) (+1 bonus).
If you are confined to the Dungeon Master's Guide for your weapon, the only other serious choices for damage are the weapon special abilities bane (DMG 224) (+1 bonus), picking whatever the DM's throwing at you a lot, and holy (DMG 225) (+2 bonus) or, y'know, unholy (DMG 226) (+2 bonus) if you're an evil swashbuckler: a lot of your foes will be evil (or good) anyway; punish them for it. If chasing just damage buy the weapon special abilities magebane (CAr 143-4) (+1 bonus) and vampiric (MIC 45) (+2 bonus) if allowed.
The flat +5 damage from the weapon special ability collision (MIC 31) (+2 bonus) is the best you're going to get, but also consider, if it's permitted, the weapon special ability fierce (AE 96) (+2 bonus) that lets the weapon's wielder to take a penalty to his Armor Class up to his Dexterity bonus to add the the penalty's absolute value as a bonus to the weapon's damage.
Although others may disagree, most of the other damaging effects from the DMG and elsewhere inflict energy damage that a high level creature's energy resistance will easily absorb, employ effects high level foes are often immune to (e.g. ability damage and ability drain, critical hits, negative energy effects), or have saving throw DCs that are too low to be viable.
Effects That Don't Inflict Damage, But Take a Look
The weapon special ability dispelling (MIC 33) (+1 bonus) et. al. will make you popular with your group even if you aren't inflicting a lot of damage. The same goes for the weapon special ability revealing (MIC 42) (+1 bonus), which eliminates miss chances for your party; in high-level play miss chances are commonplace, and everyone will thank you even if you hit only once.
The elemental power weapon special abilities from DMG2 254-5 et. al. range from a +1 bonus to a +4 bonus and permit summoning of an elemental of increasing size based on the bonus purchased. Being an elemental-summoning swashbuckler may sound strange, but the value of minions with cool powers can't be overstated--ask any necromancer.
I don't like abilities that allow saving throws nor do I like abilities relying on critical hits, but the weapon special ability prismatic burst (MIC 40) (30,000 gp) is an exception to both. The flat cost means it's possible to add it to a weapon that's already full of other bonuses. The weapon special ability sending (LE 152) (+4 bonus) is also valuable, despite only activating on a natural 20 and a successful critical roll; a no-saving-throw teleport effect versus a high-level foe is more likely to remove him from battle than almost any other effect, although by the time this is avaialable most foes should have a way of returning to the battlefield shortly.
I've not heard of a DM actually allowing the weapon special ability smoking (LD 180) (+1 bonus), but I suggest it because it exists. It's a defensive ability, but a spectactular one, and defensive abilities keep you alive long enough to use offensive abilities. The weapon special ability spellblade (PG 120) (6,000 gp) is just as cool; pick a targeted spell the DM loves, ignore it, and even huck it back at the caster.
The weapon special ability Keeper's fang (ECS 266) (+4 bonus) renders creatures you kill with the weapon unable to return from the dead via the spells "resurrection, raise dead, reincarnate, or similar effects"; the weapon becomes evil and makes you look like a jerk to some folks, but this is such a powerful ability in any typical Dungeons and Dragons campaign that its utility can't be ignored.
Don't Neglect Accessories!
A broken weapon made from aurorum (BE 38) (+4,000 gp) can be made whole as full-round action, but a weapon made from riverine (Sto 128) (+2,000 gp/lb.) is just immune to damage.
A weapon made from morghuth-iron (AE 14) (+4,000 gp) is constantly naturally poisonous, but the poison's saving throw DC is low, the weapon's wielder takes a -1 penalty to attack rolls and damage rolls with the weapon, and many high-level creatures are straight-up immune to poison. This is, however, far cheaper than many effects, and there's no use limit.
A weapon with the template pitspawned (DMG2 278) (+1,000 gp; 0 lbs.) grants the wielder a +2 bonus to critical rolls.
A wand chamber (Du 34) (100 gp; 0 lbs.) is a space in the weapon for a wand which can be used without drawing the wand; perfect if you've ranks in the Use Magic Device skill. A hilt hollow (Du 33) (300 gp; 0 lbs.) is a space in the weapon for a potion which must be extracted but it's easier than normal. Get both. An oil chamber (Du 33-4) (1,000 gp; 0 lbs.) is expensive, but can hold an oil of greater magic weapon [trans] (PH 251-2) (3rd-level spell at caster level 20) (DMG 230) (3,000 gp; 0.1 lbs.) or ghostoil (AE 34) (50 gp; 1 lb.). A triple weapon capsule retainer (CAd 121-2) (450 gp; 0 lbs.) holds 3 alchemical weapon capsules (CAd 122), which do everything from more damage to silvering your weapon on the fly.
You'll want a weapon with at least a +3 enhancement bonus (not just a +1 weapon with at least 1 additional +2 bonus or 2 additional +1 bonus weapon special abilities!) if planning to attach the most powerful augment crystals (MIC 221). Start with the crystal of return (least) (MIC 65) (300 gp; 0 lbs.) now if you've not the feat Quick Draw (PH 98) or another way to draw a weapon as a free action. Purchase more augment crystals as needed for the campaign.
Suggestions
All bets are off if the campaign allows more sources than these.
- A +1 bane (humans) holy spell-storing adamantine rapier (53,320 gp; 3 lbs.) if you can only use the Dungeon Master's Guide.
- A +1 bloodstone collision dispelling impaling prismatic burst spell-storing vampiric adamantine rapier (195,320 gp; 3 lbs.) if you can use the Dungeon Master's Guide and the Magic Items Compendium. Perspective: This weapon costs nearly two tons of gold.
Your question revolves around the mechanical quality of various options, and I will therefore give an optimizer’s perspective to the issues. I will use words like “should” or even “must” without qualification, so I am stating up front that this entire answer is qualified as applying if you want to optimize your character.
Unfortunately, your question of regular fighter vs. sneak attack thug is problematic. Because of the realities of 3.5, which favors heavy multiclassing for martial characters, this is a false dichotomy. Thus, I’m going to introduce my answer with a significant tangent into metagame theory surrounding the fighter class. I consider this critical background information to discussing the sneak attack thug.
Why take fighter levels: Feats and BAB
The fighter is a weak class; feats are all he gets. Feats are valuable, but class features are (or should be) more so. The fighter is also a full-BAB class, which may matter to you but may not. Generally, these features are most critical when it comes to qualifying for prestige classes.
Bonus feats
In core, there simply aren’t enough feats that are good enough to justify getting only feats as your class features. Outside of core, there are more than enough feats, but the alternatives to fighter get that much better. In other words, (the regular) fighter is a class you only take if you are desperate for feats and cannot lose any BAB (if you can lose BAB, cleric, monk, and psychic warrior are often more effective ways to get feats).
The only time you should be “desperate” for feats is when you want to use a prestige class that requires a lot of them.
Base attack bonus
As for BAB, it’s important but not the be-all, end-all, unless you’re aiming to enter a prestige class that has BAB as its primary “gatekeeper” (that is, you can enter the class as soon as you have enough BAB, so missing out on BAB directly delays entry into the prestige class). If you want to enter a class that requires BAB +3, but 8 ranks in a skill, missing some BAB won’t matter much because you wouldn’t be able to enter until you got the 8 ranks anyway. On the flip side, if a class requires BAB +5 but 4 ranks, missing a BAB puts you a level behind, which is a fairly big deal.
Conclusion
So ultimately, fighter is a class that is best used to ease entry into prestige classes. In low-level games, where feats are more scarce, two levels (for a feat per level) can be good, too. But usually, you get enough feats to get the ones you actually want without needing fighter levels, which means those levels are better spent elsewhere.
Reality: fighters multiclass
Because fighter levels are primarily useful for entering prestige classes, it almost goes without saying that fighters should not literally be Fighter 20. In reality, they shouldn’t actually be more than Fighter 2 most of the time; a feat-per-level is solid; a feat-every-other-level is not. But most prestige classes cannot be entered at level 3. Thus, you need other classes.
Multiclass Penalties
Most groups do not use multiclass penalties; they are ineffective at doing what they were intended for (limit multiclassing) and many groups feel that was an undesirable goal in the first place (multiclassing is one of the biggest strengths of the d20 system).
That said, as a Fighter 2, you don’t have to worry about it. You do not suffer multiclass penalties as long as all your classes are within one level of each other, which means you can be Fighter 2, Fighter 2/X 1, Fighter 2/X 2, and Fighter 2/X 3 (or Fighter 2/X 1/Y 2 or whatever) without any multiclass penalties. Prestige classes also do not count, so if you enter a prestige class at 6th, you’ll never see a penalty.
Typical options: barbarian, cleric, ranger, warblade
Barbarian and cleric are two of the best single-level dips in the game. Barbarian 1 gives Rage, and with Complete Champion, Pounce. Cleric gives a smattering of spells, two domains (which may mean two bonus feats, or things you can’t get as feats), and Turn Undead which can be used with Divine feats. Complete Champion again improves that option, adding the excellent Devotion feats as alternatives for Domains, including the fantastic Travel Devotion. Because of Pounce and Travel Devotion, basically every melee character ever should have at least one level of either barbarian or cleric if Complete Champion is in play.
If fighter is your choice for entering prestige classes that require a lot of feats as well as BAB, ranger is your choice for entering prestige classes that require a lot of skill ranks as well as BAB. Full BAB and 6+Int skills is solid. The actual ranger class features are fairly meh, but if you need any of those feats, hey, more free feats.
Warblade from Tome of Battle is an excellent class, and it multiclasses very nicely (half your non-warblade levels count towards your warblade level for the sake of the warblade’s maneuvers). It’s often seen as “what the fighter should have been,” but if you need a bunch of feats, taking fighter levels before entering warblade works quite nicely.
Sneak Attack Thug and Rogue
What I’ve established, hopefully, is that you should not compare a Sneak Attack Thug 20 to a Fighter 20; neither option is likely or desirable. Rather, you’re talking about a Fighter 2/something 3/prestige class 10/another thing 5 or something, and wondering how the sneak attack thug fits into this picture.
Some basic facts about the sneak attack thug
The Sneak Attack fighter is better in combat than a (core) rogue. He arguably gets 1d6 more Sneak Attack (thanks to the bonus feats on both 1st and 2nd level), he has full BAB so iterative attacks come online sooner. The thug is more skilled than a regular fighter by a fair margin, though far, far less so than the rogue.
But ultimately, the Sneak Attack thug’s only schtick is combat, and there are better ways to do combat than Sneak Attack. Simple example is a mounted fighter/barbarian charger with a lance and Power Attack. Another good one is the so-called horizon tripper, taking advantage of Improved Trip’s excellent lock-down by using Combat Reflexes, and comboing fighter, barbarian, and ranger in order to enter horizon walker for excellent mobility.
Considerations of the rogue
Meanwhile, the rogue is generally seen as a higher “tier” class than the fighter. In combat, the class is lackluster; Sneak Attack is non-trivial to set up, relies on feat-intensive dual-wielding for optimal damage, and even with all that it doesn’t keep up, damage-wise, with a good charger.
But the rogue is still better. All a charger can do is damage; a rogue can do so much more. The thug adds in a fair few more skills, but the class skill list is still paltry compared to the rogue’s, and the rogue probably has more than twice as many skill points. Most importantly, the rogue gets Use Magic Device in-class, and that skill is amazing.
Conclusion
If you do not need feats very badly, you don’t really want (regular) fighter levels. The sneak attack fighter replaces these with Sneak Attack; not a bad trade, but the rogue gets so much more along with Sneak Attack.
So you should only take fighter levels if you really need BAB and feats or Sneak Attack. If you’re a rogue, stick with rogue unless you need BAB for something. If you want some BAB, but aren’t hurting for feats, a sneak attack thug level will get you BAB without costing you Sneak Attack, and it’ll hurt your skills at least somewhat less. If you really need BAB and feats, then regular fighter is your best bet.
Best Answer
Personally, I’d say you’re about done with fighter and swashbuckler
I try to avoid taking more than 3 levels of swashbuckler (insightful strike is its best feature) or 2 levels of fighter (a feat per level is OK; a feat every other level is pretty weak). I’d say it’s probably a good time to leave those classes behind.
The exception is if you take, e.g. Daring Outlaw (see below) to improve these classes. The Zhentarim Soldier ACF can also do wonders for the fighter class (up to 9th level anyway) if you have the Charisma and Intimidate ranks for it.
Classes
The best answer is warblade (but you don’t have that allowed)
Just for the sake of anyone else reading this, the warblade (Tome of Battle) is perfect here: he’s flashy, highly-skilled, and makes good use of Intelligence (and he gets 4+Int skills). White Raven makes him an excellent battlefield leader.
You already have Int to damage: factotum adds Int to (almost) everything else
(I just noticed you don’t have factotum listed either; that’s a real shame. Again, leaving this here for future users who do)
Factotum (Dungeonscape) sounds really perfect for your character here. They do gain a few spells (and some Supernatural abilities), though there are homebrew variants that can remove them. More importantly, the factotum’s whole schtick is “I add Intelligence to everything.” Like all Strength and Dexterity skill and ability checks (e.g. Athletics, Acrobatics, Stealth, Initiative) at level 3. In fact, the only notable thing that factota don’t add Intelligence to is damage: that you already have from swashbuckler’s insightful strike.
And a factotum is always the man with the plan, even if he’s actually just making it all up as he goes along. Seems like a pretty good guy to follow.
See this question for more information on using the factotum class well.
You may already qualify for chameleon, and it’s pretty good
You may qualify for the chameleon prestige class (Heroes of Destiny or here) based on Able Learner (depends on whether or not you’ve been putting points in the skills you need). While the best feature of chameleon is their spellcasting options, you don’t need to use them. Two levels of chameleon gets you the wonderful “floating feat,” a feat you can change every day. A third level can get you some sneak attack damage, which is useful (see below re: Daring Outlaw).
If you qualify for that, you might also make a good master of masks
This prestige class (Complete Scoundrel or here) isn’t very good and is probably way too specific for you: you want to be a leader of men, not hiding behind constantly-changing masks. But if you take just one level (i.e. only get one mask), and choose the gladiator mask, you get to be Maximus. You become proficient in every weapon ever, which is pretty awesome, and we all know how Maximus leaves everyone entertained.
Dread commando is fitting, but not very strong
The dread commando prestige class (Heroes of Battle or here) is full-BAB and gets sudden strike, which is the weak version of sneak attack (and stacks with sneak attack for qualifying). Requires Dodge and Mobility, which is a shame since they’re pretty weak and you should have ranks in Tumble to avoid AoOs anyway. Mobility, at least, can be gotten as an armor special ability (and the rules do allow you to qualify using items, but make sure DM allows it), but it’s quite expensive for your level.
Note that there are several feats (Midnight Dodge from Magic of Incarnum, Expeditious Dodge from Races of the Wild, Desert Wind Dodge from Tome of Battle) that count as Dodge and are better. Still not good, but better. Worth considering.
Anyway, dread commandos are skilled fighters, and the bonus damage is good for a finesse build, and you get some team-based bonuses. So fitting. But it’s a weak form of bonus damage and the team bonuses are pretty small, so not very good.
A little bit of bard could work
Bards require ranks in Perform, but unless you use their spells they don’t actually need Charisma. Just one level for inspire courage would not be a bad idea for the sake of being all leader-y. You can just ignore the cantrips that you get.
See this question for thoughts on making the most of the bard class.
Knight is OK for a few levels
Knight (Player’s Handbook II or here) is heavily-armored and full-BAB, and makes some solid attempts to protect others (e.g. test of mettle). Unfortunately, the knight’s code is extremely strict, even stricter than the paladin’s in a lot of ways.
It’s often said that knight has five good levels: 1, 2, 3, 4, and 20. If you go for knight, test of mettle and bulwark of defense are probably your best bets.
If you can, refluff a barbarian
Instead of rage (or ferocity or whirling frenzy, which are probably more appropriate to you), call it something else: In the Zone, Focus, something. Refluff it as bullet time or something; the mechanics still work for that (particularly ferocity or whirling frenzy, which actually do make you move faster). One level in barbarian gets you these great features, and if you have Complete Champion available, you can also swap fast movement for pounce via the lion spirit totem alternate class feature, which is a great deal.
This doesn’t directly impact leadership skills, but it gives you a lot of martial prowess to back up your leadership.
Marshals are OK if you’ve got great Charisma
If you already have very-high Charisma (16-18 before items), marshal (Player’s Handbook II) is worth it for the minor auras that add that to various things. But since you can change your minor aura whenever you like, and the major auras are weirdly weak, I don't think you need more than one level.
Legendary leaders certainly fit the bill—if your DM is using the Commander rules
Legendary leader (Heroes of Battle) gives some solid abilities on an OK chassis. The problem is that it depends on the DM using the Commander rules found in Heroes of Battle, and in my experience, most don’t. Without them, a couple of abilities don’t really make sense.
If you do go this route, note that Iron Will can be bought for 3,000 gp (Otyugh Hole, Complete Scoundrel). Many DMs won’t allow it, but it’s definitely worth asking if you can. 3,000 gp is a bit much for a +2 bonus to a single save, but as something that counts for prerequisites, it’s a steal.
Feats
Daring Outlaw would improve your damage
The Daring Outlaw feat (Complete Scoundrel) stacks your swashbuckler and rogue levels for grace and sneak attack. You need 2d6 sneak attack damage to qualify, which means three levels in rogue, or a level in rogue and a level in something else that gives sneak attack (or an analogue like the ninja’s sudden strike or the scout’s skirmish; both from Complete Adventurer).
Note that a dread commando (above) could take Daring Outlaw because sudden strike stacks with and counts as sneak attack for prerequisites. This will give you +2d6 sneak attack dice from swashbuckler levels, which is nice, and allows you to consider going back to swashbuckler for more.
Daring Warrior isn’t too good
It stacks swashbuckler and fighter, two classes you already have, which makes it seem appropriate, but they only stack for the purposes of grace and qualifying for fighter-only feats. With the exception of Weapon Supremacy (Player’s Handbook II, requires Fighter 18), the fighter-only feats are pretty weak, and grace isn’t too great.
Knowledge Devotion is pretty solid
If you have Knowledge skills, it’s an attack and damage bonus. Just worth mentioning because it’s a good feat that might fit the character. Depends whether or not your wit is backed up by real knowledge, though, since Knowledge Devotion does require a fair amount of, ya know, devotion to knowledge.
Conclusion
A bunch of dips for useful abilities
I like Barbarian 1, Bard 1, Chameleon 2, and Master of Masks 1 best of the options presented that are on your list of legal material. I wouldn’t take more levels of any of these classes, however. That gets you to 10th-level, anyway. After that, I suppose dread commando and/or legendary leader are probably your best bets.
The simple option: Daring Outlaw and dread commando
The other option is to not bother with any of that hodgepodge and just go Swashbuckler 13/Fighter 2/Dread Commando 5 with Daring Outlaw. That gets you full BAB, 7d6 Sneak Attack, and 3d6 Sudden Strike. Of course, that assumes you can get Dodge and Mobility... Anyway, it will make you a reasonably effective melee combatant and give some minor bonuses to those around you. It’s not the best build available but it does have a certain elegance.
I really do have to mention warblade again
If you can get it allowed, I have to mention again how perfect warblade is here. With a start of swashbuckler 3/fighter 2, you can do really well by taking three other classes, and then taking warblade at 9th to start with an Initiator Level of 5, thereby starting with 3rd-level maneuvers and stances. My preferences for those three levels would be Factotum 3, Chameleon 2, Barbarian 1, Master of Masks 1, and/or Bard 1 (such that they add up to three, of course). For bard, Song of the White Raven becomes your obvious choice as 9th-level feat.