This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Tortall Universe
The fourth book in Protector of the Small series has children being kidnapped by an evil magician so he could kill them and put their souls in metal killing machines. Not to mention his treatment of them beforehand. Borderline pedophile, anyone?
The giant spider people. You know, the ones that eat kittens.
They also will cut off their victims' limbs and then web the wound to keep them from dying before they come back for another bite.
The Stormwings aren't inherently evil they're certainly creepy. (They have the bodies of giant hawks, but made of razor-sharp metal, and the upper bodies of humans and pointed teeth. They smell like rotting flesh, and were created to desecrate bodies killed in battle to try and discourage people going to war.)
The Chamber of the Ordeal, where squires go for the Ordeal of Knighthood. Sure, it's more or less benevolent, in a Good Is Not Nice way, but that doesn't keep it from being terrifying. Especially once it's proven that the entity within's powers extend far beyond that little chamber. Added bonus: the aspiring squire can't speak or scream while inside.