What the hell is wrong with you people!? You're missing one of the most nightmare-inducing enemies in most of our childhoods!
Just that entire area was nightmare inducing. Thank god as a child I never got that far. We accidentally got rid of the game before I was 5, and so I never got to experience getting past anywhere but the first dungeon.
Also, the Floormasters in Wind Waker have always freaked me out. They still do, because I have no idea when they'll pop out of their hole of darkness, only to grab me and try to drag me into it.
I've never really been scared of the Re-deads. They were never really that scary.
When I played Sims (original) as a child, my sisters and I would freak out whenever the Grim Reaper would appear. That was one of the scariest things because the game was based on like real life, and watching someone die was just horrifying.
I really don't remember anything scaring me in Mario games. There isn't a lot of things in it that can scar-I lied. I almost pee'd my pants when I saw Mimi in SPM turn into her true self. That and the music gave me horrible nightmares. I literally was just entering random rooms so that I wouldn't have to deal with her or that horrifying music. So creepy.
Pikmin always freak me out, especially in Pikmin 2. Some of those enemies are just horrifying. LIke the Smoky Blogg or whatever from the first game, and having to be scared to hell by that. I then that Water Wraith or whatever in that one blue Pikmin Cave and having to deal with that nightmare. And of course the Titan Tweevil final boss and the music making it sound scarier than the boss really is (though that flamethrower is definitely not a pleasant sight). Oh, and the time limit always make things really scary, especially as a kid playing Pikmin for the first time.
And now let me touch one game that definitely made me freak out a lot - Majora's Mask. That game as a kid gave me nightmares, just looking at the Moon and having to witness what happens when you don't turn back time. Then I was always freaked out by how scary Majora looked, and then the statues from Elegy of Emptiness were definitely creepy. Some of the bosses were definitely horrifying, like Gyorg. Of course, nothing made it scarier than the time limit and the final chamber where you face all of Majora's forms.