The Dead Hand from The Legend of Zelda: Ocarina of Time.
The first thing that grabs your attention when you enter the room are these long bloody arms appearing out of the floor, until one grabs you and the Dead Hand appears. The hand would hold you in place, allowing the Dead Hand to inch over there in a slightly terrifying manner, with its head pointing straight up, until it reaches you, bends its head down and pulls its jaw
really low to give you a nasty bite.
Possibly the scariest boss I met.
Nightmare, Metroid Fusion
I found the nightmare a
lot more frustrating than scary. The nightmare actually looks like something you would find in a typical Metroid game.