Oh, plenty of them.
Deus ex: hr - pacifist ninja, was actually pleasantly surprised there was an actual trophy for it
Batman: AA - maximum efficiency, must do all stealth sections by taking down each consecutive opponent without letting them discover a single collared body, in minimum possible time.
Pokemon emerald: nuzlocke, you are only allowed to capture the first random encounter in an area, and may release any Pokemon that faints.
And if we're counting multiplayer, plenty of ridiculous stuff in dota. "Naked" heroes, my signature dagger and butter sniper, kills only allowed with Dagon couriers, etc etc.
Currently doing one on a Pokemon black umm, "virtual machine", where the game is altered so that none of your pokes gain any do. Quite fun already, but I make it a little bit more interesting by sticking to multiplayer rules (no free switches after fainting opponent poke, and no trainer items allowed in battle like potions)