As mentioned in the spell casting section, you can use /cast to cast your pet's abilities by name. In fact, Blizzard had to change the name of the Mage elemental's Frost Nova to Freeze because there was no way to use it in a macro. :P But as everyone with a pet is aware, that's nowhere near the end of the line for pet control. Luckily the Burning Crusade patches brought us a host of new pet commands.

/petattack, /petfollow, /petstay, /petpassive, /petdefensive, and /petaggressive all correspond to the basic control commands on your pet bar. Additionally we have /petautocaston <spell> and /petautocastoff <spell> which activate or deactivate, respectively, your pet's auto cast for the named spell. There is no command to toggle auto-cast, but see "Simulating button clicks" below for a workaround (patch 2.3 will add /petautocasttoggle).