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.