See Part one (Attack, Follow and Move To) or Part two (Aggressive, Defensive and Passive) for pet commands and stances.
Besides pet commands and stances, your pet will have several "active" abilities or talents that you will need to control. Some will be species-specific (such as Prowl or Pin), but most will be shared abilities between all pets, or within the pet families of Tenacity, Cunning and Ferocity.
Shared pet abilities:
Growl - Generally, you should have Growl on autocast when your pet is tanking and off if not.
One exception to this would be in PvP, where Growl can be used to your advantage by manually Growling at player pets, taking their focus off the player until your opponent redirects them.
Cower - You can leave this on autocast if your pet will be taking some damage and you don't want to worry about it, although I highly recommend not doing so.
The main reason is because if you don't have Improved Cower, your pet will take a 50% movement speed hit - not good if you're trying to switch targets or pull your pet out of danger quickly.
The second reason is that Cower will only autocast when your pet's health dips below 40%. Occasionally there will be times when you can pre-empt incoming burst damage to your pet, so you may want to save the cooldown for those times.
Bite/Claw/Smack - Every pet has one of these abilities, which are pretty much all the same spell. This is a "Focus dump" ability, which means any spare focus your pet may have will be used by casting this spell.
Usually, you would want this on Autocast, as the other pet abilities that cost Focus have a longish cooldown and the Focus would be wasted. However, if for some reason your pet is constantly out of Focus, or you want to make sure your pet will have Focus for when you really need it (a stun or CC ability in PvP, for example), you can turn Autocast off.
Dash/Dive or Charge/Swoop - These aren't pet spells, but talents that are common and useful enough for most people to have at least one pet specced into. Keep autocast off, otherwise the ability will get used every cooldown and waste Focus even if your pet isn't moving.
Thunderstomp - For AoE tanking, this talent can be kept on autocast. If some kind of crowd control is required (or if you don't want your pet pulling aggro on mobs), this needs to be turned off.
Intervene - You may want to macro this, as you need a friendly target to cast it on. A simple macro may look something like this:
/cast [@player] Intervene
...for yourself, or perhaps:
/cast [@mouseover] Intervene; [@player] Intervene
...which will cast Intervene on your mouseover target, or yourself if you don't have a target.
Roar of Sacrifice - See above for Intervene. This is also a Cunning ability.
Last Stand - If you expect to use this in a hurry, I would recommend pulling this out onto an easy-access place on your pet bar, or creating a macro and pulling it onto the player bars instead. Although it won't be used often, trying to find it in your spellbook can be annoying.
Taunt - See above for Last Stand. In addition, make sure your pet is attacking the target you want it to Taunt before you hit this spell.
Carrion Feeder - Unless you use this a lot and don't need all four spaces for pet abilities, you can leave this one in your spellbook.
Bullheaded and Roar of Recovery - See above for Last Stand.
Roar of Sacrifice - As above for the Tenacity talent.
Wolverine Bite - In general, this can be left on autocast as for Bite/Claw/Smack. Again, if you find you need to save Focus, you can turn autocast off.
Heart of the Phoenix, Call of the Wild and Lick Your Wounds - See above for Last Stand.
Rabid - See above for Wolverine Bite.
That's it for now. Stay tuned; I will be covering species-specific pet abilities and how to organize your pet bar (Blizzard really needed to give us more than 4 slots on that thing...) in another post.