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.

Dual wielding daggers does scale way better with your sneak attack than using only one rapier.

At first if all attacks hit the damage calculation would be:

$$ \text{Two Daggers}: 2d4+\text{DEX}+\text{SNEAKATK} \\ \text{Rapier}: 1d8+\text{DEX}+\text{SNEAKATK} $$

With Dex = 3 and Sneakatk = 1d6 that would be:

$$ \text{Two Daggers}: 6-17 \text{(Avg. 11.5)} \\ \text{Rapier}: 5-17 \text{(Avg. 11)} $$

Variable Hit Chances:

The problem is, that not all attacks hit.

We know that daggers and rapiers use the same attack bonus, thus having exactly the same chance to hit.

$$ \text{Two Daggers}= \text{Hit Chance}\times(1d4+3)+\text{Hit Chance}\times(1d4)+\text{SNEAKATK}\\ \text{Rapier}= \text{Hit Chance}\times(1d8+3)+\text{SNEAKATK} $$

Calculation for Sneak Attack:

If we assume, that every hit is eligible for sneak attack, we can add the damage to the daggers if any of the two attacks hit. If my math does not fail me that calculates as follows: (For two Daggers)

$$ \begin{align} \text{One Attack Misses} &= (1-\text{Hit Chance}) \\ \text{Both Attack Miss} &= (\text{One Attack Misses})^2 \\ \text{Sneak Attack Chance (NOT Both Attack Miss)} &= 1-(\text{Both Attack Miss}) \\ &= 1-(1-\text{Hit Chance})^2 \end{align} $$

Also let us talk in average damage for ease:

$$ \text{Two Daggers}: \text{Hit Chance}\times(8)+(1-(1-\text{Hit Chance})^2)\times(3.5) \\ \text{Rapier}: \text{Hit Chance}\times(7.5) + \text{Hit Chance}\times(3.5) $$

Base Damage:

Regardless of HitChance the daggers deal more damage in average. As the HitChance can never be less than 0.05:

$$ \text{Hit Chance}\times8 > \text{Hit Chance}\times7.5 $$

Sneak Attack damage:

The damage would be equal in both cases, so the relevant part is the trigger chance. Assuming the attacks are eligible for a Sneak Attack, the relevant part would be whether you hit or not.

When attacking twice, your chance to hit is higher than when only attacking once.

$$ (1-(1-\text{Hit Chance})^2) \geq \text{Hit Chance} $$

Assuming 0 < HitChance ≤ 1

Proof (Thanks to @Glen_b):

$$ 1-(1-H)^2 = 1-(1-2H+H^2) = 2H-H^2 \\ = H+H(1-H) \geq H \forall 0\leq H \leq 1 $$ with equality only possible at the endpoints and a maximum difference at $$H=0.5$$

Here is a graph to visualize the chances that you can apply your sneak attack damage:

Y = Sneak Attack Chance; X = Hit Chance per Attack; Red = Two Daggers; Blue = Rapier

Thus, two daggers are better with and without sneak attack.

Here is another graph visualizing the average damage for both weapons (Assuming +3 Dexterity modifier, 1d6 sneak attack, no magical bonuses, all attacks eligible for sneak attack.)

Y = Damage; X = Hit Chance per Attack; Red = Two Daggers; Blue = Rapier

Opportunity Costs

Through OPs comment on another answer, I know his rogue is level 2. This means he could use his bonus action to Dash, Disengage or Hide.

Later on, depending on your subclass and table rules, you might gain Feats or other class features like Fast Hands which require your bonus action. So, why would I take the Two Daggers instead of the Rapier? This would trade in positioning possibilities or other maybe useful opportunities for a measly 0.5 damage.

While the damage difference might appear to be 0.5 in average, the real advantage of dual wielding comes with the sneak attack chance.

Look at it this way:

If you have only 50% hit chance the difference would be

$$ (0.5\times8+0.75\times3.5) - (0.5\times(7.5+3.5)) = 1.125 $$

The daggers now deal 1.125 damage more in average.

Same scenario, but without sneak attack:

$$ (0.5\times8)-(0.5\times7.5) = 0.25 $$

Only a 0.25 damage difference. This gap increases drastically as sneak attack damage increases.

So your goal is to get your sneak attack damage through. If your first attack hits, your rapier deals in average 2 damage more than the dagger, but if the first attack misses you deal no damage with the rapier, while dual wielding gives you another attack to possibly deal your sneak attack damage.

Why is this so important?

When looking at your weapon attack damage, how does it scale?

• Your Dexterity modifier might go up (but would benefit both weapons equally)
• Your sneak attack damage increases with your level (better for daggers, because of higher hit chance if you attack twice)
• You may get a magic weapon

The 2 Avg. damage difference from the damage dice, if the first attack hits looses its relevance while the increased chance of sneak attack gains in relevance.

Let's look at a level 5 rogue who used is ASI on Dex (+4) and has now 3d6 Sneak attack damage. With a 50% hit chance: [the numbers in square brackets are without sneak attack]

$$ \begin{align} \text{One Dagger: } 0.5\times(2.5+4)+0.5\times(10.5) = 8.5 \text{ [3.25]}\\ \text{Two Daggers: } 0.5\times(2.5+4)+0.5\times(2.5)+0.75\times(10.5) = 12.375 \text{ [4.5]} \\ \text{Rapier: } 0.5\times(4.5+4)+0.5\times(10.5) = 9.5 \text{ [4.25]} \\ \text{Rapier+1: } 0.55\times(4.5+4+1)+0.55\times(10.5) = 11 \text{ [5.225]} \end{align} $$

Y = Damage; X = Hit Chance per Attack; Red = Two Daggers; Blue = Rapier

Even a Rapier+1 does not reach the Avg. damage of two daggers.

Here an level 20 (+5 Dex, 10d6 Sneak attack damage) example:

Y = Damage; X = Hit Chance per Attack; Red = Two Daggers; Blue = Rapier

The damage gap increases, but to get the most out of your turn I would recommend the following:

If your first attack with dual daggers hit, accept that you might have dealt more damage with a rapier and use your bonus action to get away (improve your survivability). If this is no option you can attack another time to maybe deal 1-4 extra damage.

If the first attack misses, attack another time, this is where dual wielding shines.