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.

The alchemist's lab specifically overrides the more general masterwork tool and the masterwork artisan's tools

• Most skills don't need tools. However, a craftsman usually needs different artisan's tools for each Craft skill.
• You can buy a masterwork tool for a skill. The masterwork tool for the skill Craft is masterwork artisan's tools.
• If a specific masterwork tool is available for a skill (and you want that circumstance bonus) you must buy that instead. The specific masterwork tool for the skill Craft (alchemy) is an alchemist's lab.

Below are relevant passages from the Player's Handbook. They don't make a lot of sense when considered individually, which is why I included the above summary.

The Player's Handbook on Favorable and Unfavorable Conditions says

Give the skill user a +2 circumstance bonus to represent conditions that improve performance, such as having the perfect tool for the job, getting help from another character (see Combining Skill Attempts, page 65), or possessing unusually accurate information. (64)

Emphasis mine. The Player's Handbook later describes the masterwork tool as follows:

This well-made item is the perfect tool for the job. It grants a +2 circumstance bonus on a related skill check (if any). Some examples of this sort of item from Table 7–8 include masterwork artisan’s tools, masterwork thieves’ tools, disguise kit, climber’s kit, healer’s kit, and masterwork musical instrument. This entry covers just about anything else. Bonuses provided by multiple masterwork items used toward the same skill check do not stack, so masterwork pitons and a masterwork climber’s kit do not provide a +4 bonus if used together on a Climb check. (130-1)

Emphasis mine. Note that the list of examples isn't exhaustive and that Craft is a skill. The Player's Handbook also describes artisan's tools:

These special tools include the items needed to pursue any craft. Without them, you have to use improvised tools (–2 penalty on Craft checks), if you can do the job at all. (129)

And masterwork artisan's tools:

These tools serve the same purpose as artisan’s tools..., but masterwork artisan’s tools are the perfect tools for the job, so you get a +2 circumstance bonus on Craft checks made with them. (129-30)

Emphasis mine. Finally, the Player's Handbook describes the alchemist's lab, in part, as follows:

This set of equipment includes beakers, bottles, mixing and measuring containers, and a miscellany of chemicals and substances. An alchemist’s lab always has the perfect tool for making alchemical items, so it provides a +2 circumstance bonus on Craft (alchemy) checks. (129)

Emphasis mine. When a skill lacks a specific perfect tool, you buy a generic masterwork tool or, for a Craft skill, generic masterwork artisan's tools for that Craft skill. The skill Craft (alchemy) has a perfect tool available: the alchemist's lab. This makes both a masterwork tool and masterwork artisan's tools unavailable for the skill Craft (alchemy) in the same way you can't buy a masterwork tool for the skill Heal instead of a healer's kit. To get the +2 circumstance bonus for using the perfect tool on Craft (alchemy) skill checks you use an alchemist's lab.