So whether it's guildies with rogue alts or low level rogues just starting out, people are always asking me what is the best rogue spec in the current 4.0.6 patch.
Well from Patch 4.0.1 through 4.0.3 the simple answer was Assassination, hands down. On paper Assassination came out at roughly 4% more DPS than Combat spec while in practice, taking in to account fight mechanics (the 'on paper' results didn't take in to account needing to move out of the fire so to speak), the difference was actually somewhere in the vicinity of 10-15% or even more on some boss fights.
Patch 4.0.6 went a long way to closing the gap between Assassination and Combat and while there are still fights that have mechanics that favor one spec over another the current answer to the 'which spec is better?' question can now be countered by two additional questions that should be the basis of your decision on which spec to play on your rogue:
1. Which spec do you enjoy playing the most? and
2. Which spec do you have the best weapons/gear for?
At this stage both spec's are so close to each other that it really does come down to which spec do you enjoy playing the most, and do you have at least 346 ilvl weapons suited to that spec? (the minimum ilvl I would recommend for raiding)
I think, at least for rogues at the moment, Blizzard have done a good job of balancing Assassination and Combat so that both are viable raiding specs, giving the player the choice of which to play rather than 'play this spec or be prepared to do sub-par DPS'...which is how it should most definitely should be!
Links to my current Patch 4.0.6 Combat and Assassination Spec Guides: