Definitely check out Invisible Blade, as it removes the necessity to flank. Also, if you can hide effectively, you can do all sorts of nasty.
As for base damage... heh. I have a character who currently does 1d3-1 base damage (19-20/x2 crit). We use a crit variant where if you keep threatening on your confirmation roles, you keep rolling... well, let's just say he did 4 points of damage with a single hit. Plus sneak, of course. But yeah, crits become pointless because the best thing to do is stack as many d6s on a single hit as you can.
Other options: Shadowdancer, or other class that grants Hide in Plain Sight. Hide, move up behind someone, full-attack sneak.
Dust of Disappearance or Improved Invisibility. Same idea.
Ninja base class (Complete Adventurer): can go invisible a small number of times per day. Sudden Strike (only when flat-footed, not flanked) works _really_ well with Invisible Blade.
I actually went two levels of Monk, and convinced the GM to let me take a feat to treat daggers as monk weapons; you get the extra attack of a TWF without having to spend the feat. I'm losing the -5/-10 offhand attacks, but get to ignore the TWF feat tree. Which, btw, is _painful_.
Oh, and for the completely munchy path, see if you can use Unapproachable East (FR book). There's a prestige class in there, Tefl-something Shadowlord, that can full-attack after any teleport. Great Gods of Greyhawk, that's powerful.