First off, sorry to all the boys reading this who think "youch"
Second off, I don't know if this has been suggested, planned, or otherwise posted. I have to admit I haven't read all suggested material.
I propose some kind of system that allows the dwarves to castrate their (male) animals. Let me start by saying that I'm not concerned about the smaller animals like cats and dogs and I'm not saying have this applicable to all animals (birds, reptiles). I'm concerned about the larger farm stock. I like keeping a bunch of female farm stock (ewes, alpacas, llamas, donkeys, horses, et cetera) for their wool and milk, as well as for their meat. I find once you introduce a male into the fort all my females breed with said (lucky) male and give birth, which means I have a lot of young stock. Once one of those male young stock grows up, he breeds with the females again and I get even more young stock. I've been having to resort to killing off my young male stock before they grow up in order to control the population of my stock. A castration feature would be incredibly helpful in that I can raise my male stock, get them nice and fat, then butcher them for their tasty meats, without worrying that they will impregnate all my females.
Castration of farm stock is a wide spread occurrence in our world and I think the dwarves are smart enough to figure out "hey if you cut off the male's wingding then he can't mate with the females" (after all dwarves make babies too). It's a fairly simple procedure involving a sharp knife and a little knowledge of anatomy. I don't propose this for female stock since that gets to be a little more surgical (although I am open to the idea).
This procedure can be done by professions already in the game (animal caretaker, animal trainer) using buildings already in the game (kennels). It can give a token to the animal that designates them as sterile (genderless perhaps, or a third gender value), which can also be used for mules (or is already used for mules, I'm not sure how mules work in game). It should be able to be done with young stock and adult stock. There may be a size limit (they can't castrate a cavy boar, but they can a yak bull) and/or an animal type restriction (mammals are castratable but not birds (since they don't have the very obvious wingding for the dwarves to see)).