Quake/Quake2/Doom II/Warcraft/Warcraft 2/Starcraft/Duke Nukem3D
Those are the ones I like, I do have some others installed but either never play them or know they have PC versions like:
MacBrickout is the best brickout game I've tried. Marathon - a 3D fps which was Mac only I didn't like it much Other Mac games where I'm not aware of PC versions: Barrack and I think Mars Rising are exclusively OS9/earlier, Barrack in particular will not run under Classic environment in OSX or using an emulator like sheepshaver or basilisk 2. They may well be clones of PC games but life isn't long enough for me to look into that. They list some derivatives which have PC versions.
All by Ambrosia games, - I've always felt they did high quality fun stuff, though the few I tried are all arcade-ish.