I keep coming up with ideas that'll require cruelty to my citizens, but the complicated ones rarely come to fruition: Oilgulfs (a perfect randomly generated name) was going to be a candy-mine blowout from an offshore platform before crashes and terrible FPS forced me to abandon, the pony vault experiment's been on the back burner for months, and I've started three fortresses so far with the intent of running a segregated society only to build an egalitarian paradise.
Oh, there are little incidents like the time I executed a vampire that'd almost finished its sentence by walling it into a room and shooting it repeatedly with a ballista or the several times that, in a fit of pique, I've locked out soldiers whose dawdling or ineptitude had allowed their squads to be killed, but the former was a kindness compared to a lifetime without booze and the latter permitted the dwarves (and one pony, at Friendlymurders) to be remembered with honor, rather than sending them to toil at the worst of jobs in boozeless obscurity before dumping them in a pauper's grave.
My worst atrocities have all been in adventure mode (spending 36 hours murdering townsfolk with a stolen crutch, attempting to break every bone or sever every limb without letting my victim die, etc), but the deed that made me feel worst happened in my very first fortress:
Sibrek of the Sewers
It was the seventh day of Obsidian in the year 209. Sibrek Ingizmonom, a tax collector sent from the mountainhomes, had arrived in Tonerazors with the then-Countess (promoted from Baroness before she reached the gate) Alathadek in the spring of 208 and had been living quietly and unremarkably ever since. Perhaps she was feeling neglected? Maybe she had neglected to survey the mines? Whatever the cause, on this day she sealed her fate by mandating the construction of three adamantine items, despite no adamantine to be found on the map.
I'd grown to like Sibrek, but I couldn't let her subject a random smith to the vagaries of Dwarven Justice, so it was with a heavy heart that I began the construction of her tomb. I allowed her to live as long as I could, but on the 2nd of Hematite 210 her time was up. A pretense was created, taking advantage of her desire to be "one of the regular dwarves", and soon enough she was inspecting a plumbing access chamber adjacent to the nobles' quarters. While there, she pulled a lever, locking herself in the chamber.
Nobody knows what went through her head -- did she panic? did she keep a level head? did she even notice the well-oiled door sliding shut? -- but the investigators were quite certain that she pulled the second lever, opening the small service chamber to a deep pipe currently connected to the bottom of the #3 reservoir.
The control room crew shut the supply valve and started the pumps as soon as they realized what had occurred, but they all knew it would take longer to drain the system than poor Sibrek had. (They could have opened auxiliary drain valves to lower the water level, but had they done so, the duchess would have realized that the sump drain system in her quarters wasn't exactly the safety feature it'd been explained to her as.) She drowned on the fourth of Hematite, but it wasn't until several days later that the water level was low enough that a work crew could enter to recover her body.
I'd intended this to be a quick, clean death, but Sibrek took much longer to drown than I'd expected, and I felt a little bad about it as she floated there. She got her revenge, though: not long after I got her buried, and while I was working on the drowning trap near what was to be my new caravan entrance, the game became unstable, consistently crashing in mid-Malachite. Thus ended my first and only 40d fort. I like to imagine that dwarves still tell stories of how Sibrek's angry ghost haunts the plumbing deep within the ruins of Tonerazors.
Of course, just because I felt bad about Sibrek (even before she crashed the game) doesn't mean I don't take joy in slaughter. I've built some sophisticated devices, but I like the cruel simplicity of:
The Pit
Deep beneath the mighty stronghold Drownedfiends lies the Pit, an unhallowed temple to Reb Irumnohus the towering eyeless alligator and Oddom Dumatshameb the janitor whose brave sacrifice bought time to contain Reb. Prisoners, still in their cages, were taken deep into the mines before passing frightening statues and a series of lead doors. There they languished, sometimes for years. The lucky ones were eventually taken to an adjacent chamber and killed, their screams audible to their compatriots, but some were brought one-by-one to the sacrificial chamber and thrown them through a hatch. A system of additional hatches gave them a controlled and mostly-survivable descent to land on top of a dead goblin in the shallow water below. These crippled prisoners soon found they were sharing their oubliette with Reb.
Unfortunately, I'd failed to notice a tree had grown in the narrow corridor, so all Reb could do was glower and roar menacingly. In hindsight, this makes their fate all the more horrible: goblins are (if memory serves) immortal, so these victims are trapped forever, in the dark, forgotten to goblinkind, listening to the growling and snarling of a creature that Should Not Be as they lie in a corner or pace their narrow, muddy cell on limbs that were once broken and never healed right. I'd imagine they'd lose their minds after a few decades.
Addendum: The Breeding Project
I was about to post this when I realized I'd completely forgotten this. In Friendlymurders, I'd built up a decent population of prisoners despite routine executions militia training escape incidents, and I'd filled the lower dining room with piles of enemies' bones behind fine glass windows, but this atrocity started out as a mere industrial process: I'd decided to build a GCS-silk farm, and for a target I selected a random white tigerwoman (from the Fortress Defense mod).
She'd been sealed in there with a giant cave spider blasting silk at her for a while when I received a notification that she'd given birth. The cubs, friendly to my civilization, turned on their own mother in a bloody battle. She killed one, but the other newborn slew its mother. What a warrior! I had a new mascot! Unfortunately I squished it beneath a bridge while attempting to get it out.
Up to now this had been a minor atrocity and an unfortunate accident, but I saw the potential. I had my miners dig out a series of chambers between the silk farm and the prisoner storage. Each chamber was fitted with a single chain and a door to block sight to the corridor. I went through my prisoner stockpiles and assigned all the surviving female Fortress Defense creatures to these chains, and I waited. Sure enough, before long a white tigerwoman was impregnated and gave birth to several cubs. They killed their mother, of course, but it was a net gain.
Unfortunately my plan didn't pan out: while they were friendly and remained so when their people lay siege to Friendlymurders above, they were neither citizens nor pets. I couldn't find any way to move them around, and the breeding center was hidden in the deeps, where such shameful things belong. The breeding project was deemed a failure, but while the project was indeed an atrocity, it was not the most horrible part of the story.
The worst part was that after all this I kept the breeding center running.