The very last boss of Drakengard. Whoa. So incredibly nerve-wracking, but so awesome once you're done. I'd rather not detail what it is, but it takes so much patience, and pause/un-pause. Insane.

Psycho Mantis from MGS was also very well done. Not that I enjoyed it, but well done.

I want to say Pyramid Head from Silent Hill 2, but that's more of a best boss, than boss fight.