For an updated post about 3.1 Hunter Pet DPS, view my new BM PvE page.
I have done some testing on level 80 test dummies with a Cat, Devilsaur, Wasp, Wind Serpent and Gorilla.
Pet families (tenacity, ferocity, cunning) have a large part to do with a pets damage; however, pet special abilities also factor in to pet damage.
Ferocity is the best tree for PvE (dps) and PvP. That's just the way it works at the moment, and it is unfortunate that a whole pet family is inferior because the Cunning tree is lackluster.
Wind Serpent: Worst dps of the bunch (wait, isn't their a gorilla in the mix?... yes there is...). Go for the Throat makes Owl's Focus pretty worthless. Cornered and Feeding Frenzy are trivial compared to a Ferocity's 9% crit and Rabid. Wolverine Bite is actually okay in PvE (bad on target dummies), but does not make up the damage loss of the other abilities. Anyways... basically you just can't go with a Cunning pet in PvE or PvP (for min/maxing purposes)... ; (
Gorilla: 2nd worst dps of the bunch. Yes, Thunderstomp is just that overpowered, even for single target dps. I'm not sure why it hits much harder that other pet special abilities, since it also hits every enemy nearby. But there ya go, a tenacity pet that can carry its own weight in a dps fight. I thought about taming and leveling a Scorpid but just didn't see great application for one (as they are only decent vs single target long boss fights, and I only participate in few 10 mans, and no 25 man raids), not to mention, that I just do not like the tenacity pet for PvE dps situations, the Ferocity in my opinion offers much better survival options (lick your wounds & heart of the phoenix).
Wasp: Right in the middle of the 5 test pets sits the Wasp. This is my PvP pet. The Sting is just too good against mages and rogues (and the debuff is good against all for the 1200 armor ignore at level 80). However, in PvE, the Wasp seems to lose a bit of its dominance as other classes can bring their own abilities that lower enemies armor which override my Wasps sting. Basically the Wasp is good but not great PvE dps. For min/maxing, the Wasp does not cut it.
Devilsaur/Cat: Easily top dps. They are both very close in terms of dps. On a target dummy the cat wins by a small margin, but buffs help a Devilsaurs Monstrous Bite, which makes them about equal in actuality. However, there is one major flaw that a Devilsaur has... and that is Monstrous Bite, which makes the Devilsaur grow... growing its hit box with it. This makes your Devilsaur sometimes aggro other mobs or bug out (not to mention the pounding steps). Basically it is just a little too much of a hassle to bring a Devilsaur and since a Cat is about equal dps, I prefer the small and silent Cat instead of a Devilsaur.
Going with a Cat also allows you more options with speccing since you do not have to go a full 51 points into the BM tree.
Basically I'm just trying to stay interested in the game now that I have almost every piece of gear that I want and almost full honor points. Can't wait for the Arena Season 5 to begin... 17th... I feel like I'm waiting for Wrath of the Lich King all over again.