Creepiest things in Zelda? Most of them have already been discussed, such as ReDeads, Pamela's father in MM, Bottom of the Well, and the Shadow Temple and its enemies within. One thing, though, that hasn't really been talked about: Arbiter's Grounds in TP. As soon as you enter the dungeon, the music just screams "eerie." The dungeon itself was very well designed, with quicksand-type obstacles and such. Also, a throwback to OoT, the spinning blades in one room of the dungeon.
What really made the creepiness of the dungeon are the "little" enemies, the ghost rats and scarabs, the little purple things that latch onto you and slow you down, leaving you vulnerable to attacks.
Also, the traps in Arbiter's Grounds were cool, for one, in one room, when you opened a chest to get a small key, the torch would blow out and a horde of invisible ghost rats would appear. (Or
not appear, 'cuz you can't see them.
)
Let's not forget the midboss, Death Sword,
who you could only see with your wolf senses at first. After he/it was defeated, a swarm of *bugs* (gross) flies up and out of the room. And Stallord, the big boss... Who could forget walking into the boss room and meeting Zant at the bottom? The battle itself, though easy, was an epic use of the spinner, an under-used item throughout the game.
Another thing I personally thought was creepy was Kamaro's Mask in MM. The guy, Kamaro, himself was just odd. You would use the Song of Healing to heal his soul and he would grant you Kamaro's Mask, which allowed you to replicate his weird dance in front of the Rosa sisters.
One thing I remember about dancing with the Rosa sisters is during the cutscene, the soldier who guarded the western gate... Just stared at you... Has anyone else gotten chills during that cutscene?