This one's open to all game catagories. Now, I'm not talking about a game who's control was so bad it made fighting/playing hard. I'm talking about a boss that was just plain nasty, viscious, could take a beating and dish one out, and took seeminly forever before the bastard/bitch (both sexes are covered here ) finally fell.
For me, that honor goes to......
Mother Brain and Dark Force!!!!!!
Mother Brain from Phantasy Star II was a complete bitch to beat. No matter how many times you hit her, no matter the strength of the magic cast, you got your ass kicked in a big, big way.
Dark Force from Phantasy Star III gets the tying nod because of the exact same thing. It took forever to disable it's hands, just so you could start beating on its head... which was another battle in itself. While it was also a sh*t to beat to Phantasy Star IV and I, the third game had the nastiest version on it.
Special honors go to Death from Castlevania I... GOD that was an unfair boss...