I used to be very emotionally sensitive and a lot of stuff scared me when I was a kid.
But by far one of the things I remember most is http://www.youtube.com/watch?v=lEOjc76O7jQ from Majora's Mask. What scared me most about him was knowing that he was still partially human and that he needed your help. That whole experience caught me completely by surprise when I first saw it and completely traumatized me.
Ah yes, Pamela's dad.
When I was a kid I used to run up the stairs and wait on the upper level. I feared he would start walking up the stairs himself after a while.

Lots of things from video games and TV shows scared me when I was kid.
Redeads from Zelda
King Ramesses from Courage the Cowardly Dog.
The Whomps or whatever the stone men from Mario 64 were called
The Forest Temple from OoT
Big Octo mini-boss in the fish in OoT
Shadow Temple from OoT
Stalfos from OoT
.
.
.
Okay, most things from Zelda scared me back when I was a kid. xD