Think about it: They're huge, vaugely human/humanoid, have masks and tenticles for faces and lurk in dim light, which naturally increases fear due to low visibility. They shamble around in an unnatural manner and the only way to kill them is to go for the throat or with help from Midna. Link is large for a wolf when he's in wolf-form, but he's *small* compared to the Twilight Messengers. I'm not sure even with a wolf's teeth and instincts how eager I would be to face them versus trying to find an escape-route.
What's more is that it's implied in the game that they don't always just kill their prey, but sometimes *turn people into them.* After listening to Barnes talk about that, *shudder.*
REDEADS. I hate them SO MUCH!!! They're like dementors from Harry Potter but they HUG/do unspeakable things to you. Wall Masters scare the crap out of me because then I'm back at the beginning of the dungeon, and Dead Heads are just f*ing scary, OK!?!?!?
Like-Likes for sure. I would've gone into depth, but it's already been said, and I like to bring up things that haven't yet been mentioned, so I'll go into depth for another choice.
Well, can I use bosses? If so, I'd have to say that one of the scariest things you could possibly face would be Morpheel from the Lakebed Temple in TP. Just imagine being stuck in the water with that thing! It's huge, has multiple electrified tentacles, and an enormous mouth that will swallow you whole and consume you.
Also, Majora is pretty unnerving.
Oh, yeah, and the Sea Snakes in MM for similar reasons to Morpheel.
I would say either a redead (when they have numbers swarming in on you), or dead hand from the bottom of the well in OoT. I think that most of the enemies that seems really out of line with anything that is in the world, they might give me shivers. Not fear, just shivers. Fear comes from the undead. I would probably feel semi-comfortable facing anything that looks kind of normal. Darknuts for example. I wouldn't really be able to do anything unless I had a weapon, but still.
The one thing I absolutely would not be able to handle would be Skulltulas. I would probably run away screaming with soiled trousers at the sight of one. They're so big, and they're spiders. I remember in twilight princess, I HATED the forest temple, because it was crawling with them.
In case you can't tell, I'm slightly arachnaphobic.