I'm not afraid of any animaton style, but there are a few that I find a bit unsettling.
Uncanny Valley has been mentioned, and it can be very unsettling. It's worse in real life - with those creepy humanoid robots people are building (footage of those give me goosebumps) - but I find it difficult to be entirely comfortable watching 3D-animated humans that are very nearly realistic. Like, the Final Fantasy movies, or the Space Captain Harlock-movie. I spend a lot of the time with a small part of me feeling like something is wrong. Their eyes don't move quite right, their facial expressions change a bit too slowly, etc. - but on a still frame, they look human. It's weird.
I also am not fond of the animation style of things like Courage the Cowardly Dog, though that might be more of a holdover from my childhood dislike of the show itself - it, and several shows that were visually similar to it, were kind of loud and shrieky, and I was (and still am) fairly sound-sensitive when it comes to screeching noises, so I might be associating the two.
And as @NickRowler mentioned - the dead-eyed look is creepy! I find it's worse in 3D than in 2D, though.
Hahaha oh my gosh yes. The first time I watched Princess Mononoke and that boar burst out of the woods, I nearly choked on my tea. >.<