At least these things come to mind:
1: Goombas in the very first super mario bros. Yep, those slow, pixelated and stupid basic Goombas. I was really young when my dad made me play that game and I was just horrified when those Goombas were moving towards me, my dad screaming: "Jump! Kill them!"
Hrr...
2: The moon in Majora´s mask. It has creepy eyes and terrifying smile. How could one not to fear it?
3: The ghost tower (don´t remember the real name) in Pokemon yellow, red and blue, with the ghosts, posessed towerkeepers and stuff...
4: The ghost hand in Majora´s mask. Yeah, you guessed right, that one in the toilet of the hotel. It just freaks me out. I mean, it´s a man, who fell into toilet through that extremely small hole and died there. His hand combined with the comment "Paapeeer... It´s just too much. Even his "Thank you is insanely scary...