Also I was turned off of Sableye when I realised that it has such a freaky smile that you don't see in the sprites.
Ha, I actually like Sableye best when it shows its creepy smile. It's why I like the Mega. ;)
The most disturbing Pok?mon have already been mentioned, but here's a few more:
Dusclops. If you saw a Dusclops observing you from outside your window, wouldn't you be scared? Not to mention, this hollow Pok?mon absorbs anything inside it, as if it were a black hole. The unlucky victims are never seen again.
Gorebyss is another eerie example. I bet you never expected this Pok?mon to do anything as dark as jab its pointed mouth into its victims, draining their body fluids until they're nothing but husks. That includes humans.
Phantump are said to be the spirits of lost children who perished in the woods. "Their cries sound like eerie screams". That's pretty disturbing, especially when you consider just how many Phantump are out there...
Yamask's Pok?dex entry states, "Each of them carries a mask that used to be its face when it was human. Sometimes they look at it and cry." Trainers in the Pok?mon world are aware of this, yet that doesn't stop them from capturing these Ghost-types...