Pit zones are useful for executions; pit a captive goblin or other hostile over a long drop, and they're dead, no real effort required. Pitting wild animals into an execution shaft whose bottom is made from a refuse stockpile near a butcher's shop is also useful; the animal will fall, splat, and then the butcher will immediately see a wild animal's corpse on a refuse stockpile and decide to go butcher it.
However, the use I find I take advantage of most for animal pits is to make pens. You see, during the last months of 40d, I consistently played with the CatSplosion mod active, which made the playable race sapient cats, which were carnivorous, so I had to develop an efficient means of getting lots of meat without having wandering tame animals kill my FPS. The method I developed was, basically, this:
Z-level 0:
=+=
=+=
=+=
=+=
===
Z-level +1:
===
=H=
=H=
=H=
===
Z-level +2:
+++
+.+
+.+
+.+
+++
+ denotes floor
= denotes wall
H denotes a hatch over open space
. denotes open space
Link a lever to each hatch (I usually put the levers on z-level 0, directly beneath the hatch they're linked to) before you seal the pen with a constructed wall (or a perpetually-forbidden door, or a floodgate, or whatever else you want to seal it with). Dump animals in the top and let them breed. The animals will wander around that 3x1 area, spreading them out more-or-less evenly over each hatch, but since they can't path more than 2 tiles away from themselves, their FPS drain is relatively minimal. Occasionally, when you want meat/leather/other animal parts, designate all of your animals for slaughter, pull one of the levers and ~1/3 of your animals will drop down, where your butcher will go to town.
I usually make several such pens and put one species of animal in each, so I can just designate all members of that species for slaughter instead of all animals period. Basically, this design mitigates the problem of FPS loss from livestock without hindering their breeding, and solves the problem of "how do I get some out without letting them all out" by making the exit through the bottom.
If you do the design with wild animals instead of tame, you can also make the "exit" on the bottom lead directly into a deep shaft with a refuse stockpile at the bottom, to take advantage of the butchery behavior mentioned at the start of this post. Don't do this with tame animals, though; butchers won't butcher dead tame animals, only live ones.