Of course, it depends on your spec to a certain extent, and even moreso on your situation. Personally, my rogue is PvP specced, and so when I'm in battlegrounds or doing world PvP I usually run with, as Quill says, Wound and Crippling Poison (one halves healing on the target, while the other slows enemies down). Mind-numbing is also nice to slow casters down. Some rogues will say they use Deadly, but since I'm a stunlocker, I stay away from any DoTs while PvPing.
Soloing, I just run with Instant on both daggers, but mostly because it's cheapest and lets me hit hard while stunlocking. In instances, I usually can't keep a mob stunned long before someone hits it, so I'll use Deadly and something else depending on what's needed (running mobs get Crippling, casters get Mind-numbing, etc.).
But my rogue is my alt, and I'm sure plenty of you have rogue mains-- I haven't done much theorycrafting on it, and I'm sure you all have. What poisons do you use when and why?