The speed of a weapon has been the lead determining factor for its strength since the launch of WoW. Consider the Barman Shanker being a best-in-slot due to its record slowness, and Webbed Death being the only name in Mutilate PvE. Blizzard's most recent change to the proc mechanics of poisons, from a static percentage to a proc-per-minute (PPM) system helps alleviate some of the DPS vs weapon speed discrepancies that existed. However, as Rogues are a well-researched class, there will always be a "best" combination available. Slow MH with a Fast OH appears to be the best for every spec, but let's explore each individually.
For Mutilate PvE, a large portion of your damage is poison-based. Now that a Sinister Revenge will proc the same amount of poison as a Webbed Death, their poison damage is same. This is the key change that the PPM system brought: the poison damage of any given weapon does not depend on its speed. As Sinister Revenge is the stronger dagger in the physical realm, it now defeats Webbed Death in a pure DPS race. SR also has a higher average damage (top end damage is irrelevant), this means it will also cause our Mutilates to hit for more damage.
However, there are other mechanics that affect Mutilate DPS. Focused Attacks thrives on faster weapons, which tilt the tables in a quicker dagger's favor. The newly improved Deadly Poison and Envenom also prefer a quick weapon for minimum reapplication time. While SR and WD will proc the same amount of Deadly Poison over a long fight, you still want a quick weapon that will allow it to be stacked back up within the 3 second tick window.
The end result of these two mechanics move us towards the end result of: Slow MH, fast OH; but where DPS is the most important stat instead of speed. A high DPS main hand that happens to be of only medium speed (1.5-1.6) is still a very viable weapon now, whereas before it would be disenchanted or used by a Hunter.
Combat features a similar mechanic to Focused Attacks: Combat Potency. This talent alone forces us to use the quickest weapon possible in the off hand, with no exceptions. The value of off hand weapon speed to a Combat build is quite possible the highest single value placed on item speed for any class. For the main hand, a similar trend occurs. Because of the instant damage nature of Combat, using the slowest weapon possible (if all the same DPS) in the main hand becomes optimal. Anything from 2.5 to 2.7 speed could be used as a Combat MH, though DPS is more important than speed. Combat has always been about using slow/fast, however now we are not penalized for using a slow main hand as it now does the same poison damage as a fast weapon would.
An interesting fact that many Rogues are unaware of is that our finisher attacks are able to proc whatever poison is currently on the main hand weapon. This means that if you put Instant Poison on your main hand, your Envenom (for example) can proc that poison, adding to your DPS. Previously, there was a bug where Mutilate was able to proc the off hand poison twice per Mutilate, and so we put Instant on the off hand, that is no longer the case. Because finishers are affected by main hand poisons, you should always use an instant damage poison on your main hand. If Mutilate, you'll use Instant Poison as it is buffed by Improved Poisons. If you're Combat, you will rely on Wound Poison's incredibly high proc rate to carry your poison damage.
Deadly Poison's scaling coefficient was buffed from 8% to 12% in 3.1, which makes it an incredibly solid poison for every Rogue. Because it doesn't deal any instant damage, it should be placed in the off hand, so that our Instant/Wound Poisons are being used for finisher attacks. No matter what spec you're playing, you should always have Deadly Poison in your off hand (except for PvP).
These new PPM mechanics are a big boon to Mutilate PvP Rogues, whose two slow daggers are now dealing both massive Mutilate burst damage along with greatly improved sustained Poison damage. Along with the significant nerfs to the Death Knight, I believe this to be a large contributor to the current success of the Rogue in the high-end arena brackets. I can personally attest to having far higher damage when I'm running on empty (waiting for energy to regenerate) than I previously did.
Spec for your weapons:
Many years ago, when I was leveling up what was to be the first of my four Rogues, I found my first blue item. The Viking Warhammer is a random world drop, which I found from some Ogres in Ferelas. Being new to the Rogue class, I asked one of my guild mates in my all-Rogue guild for advice. Should I continue on with my 25 DPS green swords, or should I switch to this shiny new mace? I'd never used any weapon other than swords at the time. His advice was sage, and something that I've passed on to countless Rogues: "spec for your weapons".
If you're on the fence, trying to decide what spec to use, simply choose whichever spec you have the best weapons for. If you have all of the best-in-slot weapons, then simply choose whichever you enjoy more. Combat will do more damage than Mutilate if you've got Calamity's Grasp and Webbed Death vs Murder and Webbed Death. Mutilate will do more damage than Combat if you've got Sinister Revenge and WD vs Kel'Thuzad's Reach and WD. It's all about the best weapons that you have right now. Sword Combat beats Mace Combat, if you have really good swords. Mace Combat beats Fist Combat, if you have really good maces. We're still all about our weapons, and so if you're looking for your new 3.1 spec, just look at what your hands are wielding and go from there.