The Culex fight murdered me so bad as a kid. I could never beat him without Lazy Shell Peach. ; -;

The Genocide Heart fight in SaGa Frontier is still my favorite boss fight in an RPG, so I'll throw that one out there. Using the display screens to communicate its health to the player was a simple yet totally awesome idea, and the way it bounces Carnage lasers off of them when it attacks you is just . . . AHHHHHHHH!

+5 greatest genocidal robot in gaming.

EDIT: Oh, Luca Blight in Suikoden II is another one. I have no idea how I forgot that fight.