Well, there's the obvious- Dead Hand, Re-Deads- those ar at the top of my list. But scariest enemy I've seen out of a Nintendo game? Certainly Andross from StarFox 64. Uggh, it was TERRIBLE. A giant floating monkey head with disembodied hands?
I was 12 at the time when I fought him for the first time, and I was scared silly. He tried to eat you, and when he shows up, he fades in and jumps out at you, get really close to the screen, and laughs. And the worst part? At the end of the credits his face fades in and you hear him laugh again. I literally ran out of the room when that showed up.
Search Andross on google images, you'll find him.
And like Valexi said... I have to see THAT in 3D? Ugh...