The following guide is a helpful tool for hunters who would like to use their pets in end-game raids.
Introduction
All hunters should use their pets in a raid. A good pet, regardless of the hunter's talent build, can put out around 10% of the hunter's total DPS. Refusing to utilize this extra damage would be similar to giving up a 50 DPS weapon you can use in addition to your normal weapons. The only thing you have to do is feed the weapon, keep it healthy and happy, and know when to put it away.
The number one rule about using pets in raids is this - make sure you know what you're doing. Nothing is worse than having a pet in a situation it's not supposed to be in. Certain encounters require you to dismiss your pet, others require you to set them aside. There are pathing issues, facing problems, and other such things you need to keep track of if you're going to use your little friend in these instances.
Second - okay it with your guild. Most guilds will allow a hunter to bring pets with them, but mostly as a buff. 
[Furious Howl] is a good buff, and having your wolf cast it is a good way to raise DPS. If, however, you want to actually utilize your pets, that's where guilds start to get a little iffy. Hunters have a bad reputation with pets. Pathing issues aside, pets have received a (false) reputation of not dealing enough damage or not surviving long enough to be of any use.
Third - bring food. Your pet will die. This is a fact of life, and you've got to be ready for it. Bring enough food for an entire raid. If you have a meat-eating pet, then you're going to have to bring a lot of meat. Those pets that eat bread are definitely an asset, because your mage makes free food for them. I usually bring one stack of meat on a raid, and my pet eats through it quickly. Keeping a happy pet is worth a few gold.
Skills and Training
See Training your pet for further clarification on training pets and skill points.
In end game, the most useful skills your pet can be trained are the resistances. This helps them survive the most damaging aspects of the raid environment. Each 120 point resistance training costs 90 Training Points. If you wanted, you could train your pet with up to three Resistances, but this would leave you with 30 points for 1 ability. On some pets (raptors, for example) this is not that big of a deal since they get no special abilities aside from 
[Bite] and Claw. In the case of a raptor, training three resistances and claw is the best thing to do.
Each different instance requires different resistances, as is well known. Fire resistance is good in Molten Core and Blackwing Lair, Shadow resistance is good in Blackwing Lair and Naxxramas, Nature resistance is good in Temple of Ahn'Qiraj and Naxxramas, and Frost resistance is good in Naxxramas. If your guild has Molten Core and Blackwing Lair on farm status, then it would be a good idea to retrain your pet in Nature and Shadow resistance.
The other abilities a pet gets are useful as well. Pets with Dash or 
[Dive] can get into and out of battle quickly. Bite and Claw increase damage, claw is better DPS, but bite deals more damage. All pets should have 
[Growl], but turn it off for raids.
Pet Family Abilities
Pet family abilities are useful in end game as well. Saving training points for these is a very good idea. The highest rank of these abilities costs 25 training points.
Furious Howl
The most useful ability is Furious Howl. Only wolves can train this ability. Every 10 seconds, party members within 15 yards of the wolf get an increased damage on their next attack. At rank 4, this ability increases damage by 45-57 points. Wolves with Furious Howl are most often just sat next to the Hunter, the ability cast every 10 seconds, but if a Hunter with this ability is put in a group with Rogues or Warriors, it would be better to send the wolf into battle with their target.
Furious Howl rank 4 can be learned from the Bloodaxe Worg in Lower Blackrock Spire.
Screech
[Screech] is also a useful ability. This is available to bats, carrion birds, and owls. Screech is an AoE debuff that deals minor damage and lowers attack power of enemies by a certain amount. At rank 4, it decreases the attack power by 100 points. This debuff is overwritten by most other debuffs, however, so it's rare that it sticks too long. In the Burning Crusade, the debuff limit will be increased, so Screech will be more useful.
Screech rank 4 can be learned from the Monstrous Plaguebat in Eastern Plaguelands or the Winterspring Screecher in Winterspring.
Charge
[Charge] is an ability available to boars. It stuns the target for 1 second and increases the damage of the boar's next attack. At rank 6, this increase is 550 extra damage.
Charge rank 6 can be learned from Plagued Swine in Eastern Plaguelands.
Lightning Breath
[Lightning Breath] is an ability for wind serpents. This is a high-focus cost ability that deals nature damage from 20 yards away. At rank 6, it deals 99-113 damage. Note: When training Wind Serpents, be aware that those with mana bars in the wild will have higher spirit and intellect when trained.
Lightning Breath rank 6 can be learned from the Son of Hakkar in Zul'Gurub. It is possible, and quite easy, to solo tame this pet.
Prowl
[Prowl] is an ability available to cats. It puts the cat into stealth mode, and reduces their speed. The first attack out of stealth has an increased damage. At rank 3, it deals 50% extra damage immediately out of stealth.
Prowl rank 3 can be learned from the Frostsaber Stalker in Winterspring or the Jaguero Stalker in Stranglethorn Vale.
Scorpid Poison
[Scorpid Poison] is an ability available to scorpids. This ability deals nature damage over time, and can stack up to five times on the same target. At rank 4, it deals 40 damage over 10 seconds, or 20 damage per one second when stacked up to 5 times.
Scorpid Poison rank 4 can be learned from the Firetail Scorpid in Burning Steppes or the Stonelash Pincer or Stonelash Flayer in Silithus.
Shell Shield
[Shell Shield] is an ability available to turtles. This ability reduces the damage dealt to these pets by 50%, but increases the time between attacks by 43%. There is only 1 rank of this ability, and it lasts 12 seconds on a 3 minute cooldown.
Shell Shield rank 1 can be learned from Aku'mai Fisher, Aku'mai Snapjaw, or Ghamoo-ra in Blackfathom Depths, Giant Surf Glider in Tanaris, Kresh in Wailing Caverns, or Snapjaw in Hillsbrad Foothills.
Thunderstomp
Thunderstomp is an ability available to gorillas. This ability deals AoE nature damage to targets within 8 yards. It's got a high focus cost, and a 1 minute cooldown. Rank 3 deals 115 to 133 damage to all targets.
Thunderstomp rank 3 can be learned from U'cha or Un'goro Thunderer in Un'goro Crater.
Using Your Pet in Raids
Now that you know what abilities and resistances you need for the instances, the next thing to know is how exactly to use these companions in a situation which tends to be difficult for them to survive. Unlike players, they are not high on the healing list. They also cannot use consumables when they are in trouble. Their survival rests on you as a controller.
You have to know a few things about what it is you are fighting. Certain encounters it is bad to have a pet (Skeram)), others the pet will die too quickly for them to be of any use ((Sartura)). When your pet can be used, there are a few simple things to remember.
- Watch the healthbar - If your pet starts to lose a lot of health, pull it back. When they die, it's over for them. They cannot be used for the rest of that battle unless you're willing to give up a lot of time and mana to revive them. If you want to, use
[Mend Pet] when you're going to use an [Aimed Shot] every so often to keep your pet alive. - Be aware of AoE - Some bosses have AoE attacks that deal a lot of damage. If you know the timing of the action, you can bring your pet back without it being damaged. Most of the time, you'll have to accept they'll be hit. Similarly, if your pet has an AoE attack (Screech or Thunderstomp), turn it off if your raid is using crowd control. The majority of guilds don't like pets in raids anyway, and if Smokey the Gorilla breaks a sheep, they'll like him even less.
- Don't expect heals - Your pet is not on healers' priority, unfortunately. If you're lucky, they'll get hit with a quick heal or some HoT. Be glad, thank the healer, and continue to fight. If you thank the healer for giving your pet a fighting chance, they're more likely to do it again.
- Watch the pet's position - A good thing to remember is to place your pet with the rogues. Sometimes your pets are smart enough to move with the boss, but sometimes they don't move and end up right in the way of a burn or a cleave. Be aware of where your pet is, and if you see it in a compromising position, move it out of the way and reposition it.
If you remember these tips, your pet will be a great addition to any end-game raid.