This is a great topic!
For me, the top 4 would be...
1. Carnivorous "bugs", especially spiders and praying mantises. With spiders, it's more the bug (well, arachnid) itself that's creepy. Mantises don't look especially scary, but the way that they will start indiscriminately chewing on whichever part of their prey is closest to their mouths can yield some really creepy results. I once saw a YouTube clip of a mantis eating a bee face-first, until there was just a twitching brain-stem remaining... ughhhhhhhhhh!!
I will probably never get that out of my nightmares now, but it happens every day in the insect world. And I can't look away when I find something like that because although it's really horrible, my morbid curiosity gets the better of me.
2. Supernatural horror movies... those just go straight into the "nope" file for me. I don't like being startled, but it's 1,000 times worse when it's by some deranged skeletal apparition with glowing eyes that wants to eat your soul. Curiously, I'm not afraid of zombies at all, not even a little bit. It may have a ravenous appetite for human flesh, but if it can't scheme and plot and plan, has no conscious will of its own, and/or if it's mindless, I'm not afraid of it.
3. Decapitation. Like a number of Aspies I've met, I have a heightened sense of bodily integrity; I am unnerved by grave bodily injury, especially the loss of a limb. And I also value my brain. Plus, I just can't fathom what it's like to be separated from the rest of your body, so the whole notion just freaks me out.
4. Drowning / the ocean. I love oceanographic movies and I think the sea is beautiful in so many ways... but I also have a lot of respect for large bodies of water and the stuff that lives in them.