Dont forget, you can toss a vampire in the bottom of a well with an upright spike, and stab them a few times, to create a pool of their blood, which contaminates the well water and passes on their vampirism. Forbid all your booze for a month or two, turn the entire fort into vampires.
In addition to what Recon mentioned, elves and goblins, and invaders in general, make good cage occupants for dining room display areas. Dwarves like seeing creatures in cages, like a zoo for them. A zoo full of their enemies.
Someone invented a highly efficient means to separate coin stacks into individual coins to exploit the fact that individual coins can be melted down in significantly more bars than it took to produce the stack: Put visitors/invaders in a 1x1 hole in the middle of fortifications, and force them to watch their comrades die gruesome deaths, then endure the decay of their bodies. They will eventually start tantruming, and throwing the coins around, which splits the stacks up.
There was a bug with rescuing children from dark pits which I'm not sure was fixed; if you successfully take them back to their family members, they'll murder the kid because the kid is technically a member of the goblin civ. Not sure if its been fixed.
You can also recruit wild animal people by singing/reciting poetry to them and asking them to join you as an entertainer. Then return to civilization, where they will be attacked and killed for being a wild animal. Its needlessly cruel.
Create a zombie army by throwing your invaders in a death pit with a captured necromancer tucked away above and behind fortifications. Just keep throwing them in there. The necromancer will freak out and raise the corpses of the dead to defend themselves from the enemies in the pit.
Someone made a drawbridge torture arena where instead of intentionally smashing captured invaders, they would fling them around when the bridge was raised. A catapult from hell. Possibly into hell. That was quite a while ago, but it should still work quite well.
And that doesnt include the atrocities you can commit through modding. So many atrocities, I can hardly count them all.