I think 'Doom' and 'Street Fighter II' take the cake when it comes to which games have been raped by and tossed back and forth between companies to get it on every platform in existance. 'Doom' on SNES, 32x, GBA = Awful as puke. 'DoomDS' could have been a brilliant idea, since it actually could have run similar to the PC version, but these companies often don't see the obvious.
Street Fighter II on the ZX spectrum, Amiga, hell even the DOS versions (just to name a very small few, there are about 30 billion clones out there) are just abominations. Awful music, non-existant gameplay.. if the fighter is moving at 4 FPS, its a stretch even calling it a fight. The pirated NES versions (Master Fighter II and Street Fighter III) are, and I quote, "Miyamotoesque" compared to 95% of 'official' ports.
If you aren't playing Street Fighter II on a SNES, Genesis or real Arcade machine, you're not even playing SFII since the same skills don't apply.