I have thought a lot about implementing rapier and dagger.
I see several possibilities:
1. Tweaking TWF: e.g. instead of (2 x 1d6) weapons, characters could be allowed (1d8+1d4) -- (a good solution, but doesn't represent rapier and dagger fighting well.
OR: giving +1 AC if using TWF and at least one weapon is a dagger.
2. Expanding dual wielding: Allowing those who have the feat to gain +1 AC if they use a dagger as one of their two weapons (but requires feat).
3. Expanding armour options: a dagger (or cloak, lantern, etc.) can be used as a +1 shield with shield proficiency (excludes rogues, though) when that object is not used to attack in a given round. (Implementing buckler rules such as this seems a no-brainer to me, frankly, and I don't know why it's not there).
4. Skinning short swords: only works for certain classes, but calling a short sword a dagger and taking the extra damage is also possible ("Now that's a knife" [/crocodile dundee]).
I'd like an answer that made rapier and dagger good for both fighters and rogues. These are the best I have.