Mutilate, Combat, and HaT PvE Guides

First of all, if you haven't already, go to the post on level 80 Rogue Specs. There you'll see how to spec properly.

Each spec takes a little practice to get down perfectly. Mutilate will not have a perfect rotation if the fight requires movement, and will require a bit of thinking on one's feet to make as efficient as possible.

PvE:

Mutilate:
-Poisons: Instant in your main hand, Deadly in your offhand.
-Glyphs: Rupture, SnD if needed for 100% uptime
-Weapon: Of course you'll need two daggers. The faster they are, the better, because more poison and focused attacks procs is more important than harder hitting mutilates. If you have two daggers of varying speed, put the faster one in your main hand.

1 - Bring Hunger for Blood to 3 stacks before opening
2 - Open with Garrote
3 - After you've opened, use Slice and Dice.
4 - Mutilate to 4 or more combo points, and use envenom.
5 - Now, you should have a full duration SnD going.
6 - Mutilate again to 4 or more combo points, and use rupture.
7 - Repeat steps 4 through 6, using envenom to refresh SnD, and rupture before it drops.
8 - Refresh hunger for blood as close as possible to the end of its duration, to maximise energy efficiency.

-I suggest checking out Akrios' video guide to the spec.

Combat:
-Poisons: Wound in your main hand, and Deadly in your offhand.
-Glyphs: Sinister Strike, Rupture, and Slice and Dice
-Weapons: A slow main hand for stronger sinister strikes, and a fast offhand for more combat potency procs. Switching to a slow offhan before using Murder Spree is also a good idea, as long as you switch to a fast one afterward.

1 - Open with Garrote
2 - Sinister Strike to 5 combo points, and use SnD
3 - Sinister Strike to 5 combo points, and use Rupture
4 - Sinister Strike to 5 combo points, and use Eviscerate.
5 - Repeat.
6 - Use BF when Bloodlust/heroism is up, because haste is multiplicative and not additive. Otherwise, use on cool down.
7 - Use AR on cool down.
8 - Use Murder Spree on cool down.

Honor Among Thieves:
-Poisons: Wound in MH, Deadly in OH
-Glyphs: Rupture, SnD, Eviscerate
-Weapons: As with Mutilate, the faster the better. Fastest weapon goes in the main hand. Why? Because you aren't going to be using hemo nearly at all. Your damage should be coming from Evi, white, poison, rupture, in that order.

The idea here is to keep SnD and rupture up at all times, then doing eviscerates, while maintaining high energy. That is, letting your energy fill almost to full, and eviscerating. Of course a 5 point eviscerate is better than a 2 point eviscerate, but two 2 point eviscerates is better than one 5 point eviscerate, so if you have to wait too long before you can evi, then just go with fewer CPs.

1 - Open with Garrote
2 - SnD at 5 CP
3 - Rupture at 5 CP
4 - Eviscerate at 3-5 CP until SnD reaches about 3 seconds left on duration
5 - Repeat.
6 - Use BF with Bloodlust/Heroism, otherwise use on CD.
7 - Never let SnD or Rupture fall off.

Remember, practice makes closer to perfect. This is just a general guide. There is more information on Rogue PvE DPS in the Guide section of this site, RogueRogue, and the official forums.