[MENTION=18826]Bop[/MENTION] would like to see some reasoning as to why a certain pet is best for certain situations. I can see how some of those pet decisions make sense, but a reasoned opinion always brings more to the table than a non-reasoned one
Well for starters,
Mortal Strike doesn't actually increase your damage done - it decreases healing. However, you're never going to outpace a healer's healing, even with the Mortal Strike debuff. Instead, you're going to make their HPS/Mana ratio extremely inefficient. As Marks (or maybe Survival, I haven't tested yet) you can OOM a healer fairly quickly and safely. In 2's, you'd probably want to go this route with a safe healer like a priest or a shaman. In 3's, this pet would work great with a teammate that either has great CC (Lock/Mage) or that puts out really consistent pressure (Ret/Feral/Rogue), because you could potentially make it impossible for a healer to keep 1 target up through that damage + Mortal Strike
Haste pet is going to be the best damage increaser for Marksmanship. This is because Aimed/Steady Shots are really easy to LoS, so you're going to want to decrease the cast time to make it easier to tag them on enemies trying to avoid the damage. Also, since the damage is based off of weapon damage, agility is going to be less useful overall than Haste in flat DPS terms. This pet is better in a healer/dps against 2x DPS because you're going to be increasing the speed on your healer's HPS output. It's also better in 3's if your partner is a caster, since you'll have Yourself, your DPS partner, and your healer benefiting from the pet.
Stamina Pet doesn't need too much of an explanation - 10% stamina is numerically the strongest bonus out of any pet. Since we scale so well with stamina (24 health per 1 stamina in scaled PvP), 10% stamina adds an insane amount of effective damage reduction. Compared to other pets which may only give an ally 5% of some stat, Bear giving 10% stamina puts it far and above any other defensive pet. Since everyone benefits from Stamina, it makes the most sense in large-scale PvP setting like a battleground or in a 5v5 arena. However, if you're up against a double DPS team in 2's or a dangerous cleave in 3's, Stamina pet gives healers more room for mistakes when trying to keep a team up.
Primary Stat pet is probably going to be the best pet in terms of DPS. There aren't going to be too many classes that scale better with Haste (or Crit or Multistrike) than they do with Primary Stats (in fact, none come to mind). So obviously this pet lends itself well to either double DPS 2's, or a quick-burst 3's team like Thugcleave (Hunter/Rogue). Haste pet is only superior in certain situations, namely when you're against teams that are likely to LoS heavily (Marksmanship has this problem a lot in 2v2). But since the lowered cast times (admittedly not too lowered, but enough to make a serious difference as anyone can attest to who has experience with Haste stacking) make it easier to land these abilities, they are superior to pets that simply buff the damage of those pets.
Multistrike/Critical Strike/Versatility are also good options, but they're kind of niche and probably shouldn't be used as often as these 4.
Multistrike doesn't lead to as much DPS as the Primary Stat pet, and has no special benefit such as the Haste Pet (I.E., allowing spells/shots to land more consistently against kiting/LoSing enemies).
Critical Strike is an interesting choice, and some hunters even tend to favor it (@Upswag). The main idea behind Crit stacking, as I see it, is that you increase the chance of the 2nd Aimed Shot to land a Critical Strike. Since the first one is
almost guaranteed to, landing a Critical Strike on the second Aimed Shot can easily land a kill or <10% health on even tanky enemies. This is definitely worthy of investigation, but as far as my own studies into the subject go, I still think Haste or Primary Stat stacking should be more consistent for Marksmanship - Survival should definitely avoid this pet in favor of Primary Stats.
Versatility is okay if you're doing 2's with a hybrid; probably a Ret/Enhance. Since it increases their effective damage and healing, it is the best one of your pets for /them/. That being said, you gain almost no benefit from the healing increase from versatility, making it have at least one person in the battleground/comp (being the hunter himself) which it has only a half-benefit towards.