The current preferences (v1.2) are as follows:

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For Vanity Pets:

Automatically summon a vanity pet when you move: If you have this option checked, you will summon a vanity pet unless you are stealthed, mounted, dead, or in combat. This will happen when you move forward or backward, turn, use auto-run, or click the right or left mouse buttons.

Credit goes to Mikhael of Doomhammer on WoWInterface for coming up with this idea and the code to execute it.
Summon your favorite pet instead of a random pet: Available when the above option is checked and if you've designated a favorite pet. It will summon your favorite pet when you move instead of a random pet.
Do not automatically summon a pet if you are flagged for PVP: With this checked, you will never summon a pet when you move when you are flagged for PVP.

...unless you are in a PVE instance: With this option checked, you will get a pet out in a PVE instance even if your PVP flag is checked.

Do not automatically summon a pet if you are in a raid: With this checked, you will never summon a pet when you move if you are in a raid of at least 2 people. Note that you have to be in a "real" raid, not a battleground raid, for this option to kick in.
Dismiss your pet whenever you mount a flying mount or cast a flying form: This option dismisses your pet in the mentioned cases to prevent pets from getting "lost" and having to trail along on the ground behind you while you fly.

Dismiss your vanity pet when you Stealth, Feign Death, or cast Invisibility: For Hunters, Druids, Rogues, Mages, and Night Elves only. If this is checked, you will dismiss any vanity pet you have out when you cast one of these spells. If this is unchecked, your pet may give away your position or the fact that you are still alive.

Only dismiss if you are flagged for PVP: If the above option is checked, you may check this one as well. If left unchecked, your pet will be dismissed whenever you cast Stealth, Vanish, Feign Death, Invisibility, or Shadowmeld. If checked, you will dismiss your pet only when you cast one of these spells and you are currently flagged for PVP.

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For Travel and Mounts:

Enable Flight Form behavior with Smart Mounting: For Druids only. If this is checked, when you can fly, Smart Mount will cast Swift Flight Form if you have it, summon a random flying epic mount if you don't, cast Flight Form if you have neither of the above, and summon a random slow flying mount if you can't do any of the previous three.

Safe Flight: Mounting while in the air will not dismount you: Normally, when you're mounted, using any mounting function of Livestock's will dismount you. With this checked, when you're in the air, you will not dismount if you try and use a Livestock mounting function.

Allow Livestock mounting to break Stealth effects: For Druids, Rogues, Mages, and Night Elves only. If this is left unchecked, you will prevent yourself from mounting if you are stealthed, invisible, or in Shadowmeld. This is to prevent accidental mounting which would make you visible.

Smart Mounting casts Ghost Wolf / Travel Form in combat: With this checked, druids and shamans using Smart Mounting will shift into Travel Form or Ghost Wolf when in combat. If unchecked, then Smart Mounting will do nothing in combat (except dismount if you are mounted).

Smart Mounting casts Ghost Wolf / Travel Form while moving (out of combat): With this checked, druids and shamans using Smart Mounting will shift into Travel Form or Ghost Wolf if they are moving when they use the Smart Mount feature. (Shamans must have the spell talented to be instant to use this properly.) If druids are using Flight Forms with Smart Mounting, then Smart Mounting will continue to instantly cast (Swift) Flight Form if the druid is in an area where flying is possible.

Smart Mounting shifts you from caster form into Cat Form indoors: Druids only. The Feral Combat druid talent "Feral Swiftness" gives you a movement speed bonus to Cat Form, even indoors as of 3.0.2. If this is checked, when you are indoors, Smart Mounting will put druids in Cat Form so they can benefit from this movement speed boost.

Smart Mounting casts Levitate / Water Walking / Path of Frost when underwater: For shamans, priests, and death knights. When underwater, Smart Mounting will cast the appropriate spell, using the player as a target if it's a spell that casts on a target.

Automatically summon a smart mount after casting Crusader Aura: For paladins only. When Crusader Aura is cast and you are not mounted, having this box checked will tell Livestock to summon a mount 1.5 seconds after you cast Crusader Aura.

Smart Mounting casts AotC / AotP when indoors: For hunters only. While inside, Smart Mounting will cast Aspect of the Cheetah (solo) or Aspect of the Pack (grouped). If you haven't learned Pack, you will only cast Cheetah.

Smart Mounting casts AotC / AotP when moving (out of combat): For hunters only. While moving and not in combat, Smart Mounting will cast Aspect of the Cheetah (solo) or Aspect of the Pack (grouped). If you haven't learned Pack, you will only cast Cheetah.

Smart Mounting casts Levitate / Slow Fall when falling (out of combat): For mages and priests. Casts the appropriate spell on yourself when you are falling and out of combat.