When looking at the pet training window many hunters are puzzled by which to train their pet in, armor or stamina. Well it depends on what you are going to use that pet for.
When you are leveling up or using the pet for a farming/tanking pet you will want armor. It will not get hit as hard but it will also have not as much hitpoints. This will make using Mend Pet easier.
If you are using the pet for raiding you will want greater stamina. Spell damage ignores armor so if your pet is in AoEs it will die faster if it has higher armor. If you have a Shaman in your raid your pet will get a few random Chain Heals which will help with your healing.
In PvP it would probably be better to go with Stamina because you will be dealing with Mages AoEing and Warlocks dotting up your pet if its really being a thorn in their side.
Also keep in mind your pet will get a certain percent of your armor and stamina. If you are a BM hunter you might want to look into some Armor/STA gear which doesn't gimp your DPS so your pet has some survivability.
I have talked to a couple of hunters who could care less if their pet dies or not. Especially MM hunters have this mindset. Looking at raid stats, using a DPS pet, a BM hunter will get around 40-60% of their DPS from their pet and a MM hunter will get around 10-15% DPS from their pet. That is a lot to lose, especially for a BM hunter, just because you don't want to take the time to hit Mend Pet. BM hunters should spec their DPS pets into Heart of the Pheonix to give them another shot at a pet. MM/SV pets shouldn't be speced into this because their pet isnt worth the DPS hit and is a DPS hit during the casting to rez pet. Try to keep them alive instead of worrying about their death.