Rosario + Vampire/Nightmare Fuel

Kahlua was introduced. She presents herself as a nice person... which makes what she does and how she does it all the more terrifying. The best way to describe her would be as a severe Deconstruction of a Punch Clock Villain. It's perfectly possible to pity her even as she's cutting open the entire main cast with her disfigured right arm. Yeah, creepy. And to make things worse, she was like that even eight years ago, when she was barely more than a kid.
Alucard is your typical grotesque Eldritch Abomination... who used to just be an ordinary vampire. Vampires may be powerful monsters, but for the most part they're still quite civil and at worst look and act like very battle-loving humans. Imagine one of them turning into this.
Ruby's master Yukata was pretty damn creepy too, both before and after fusing with a dire-sized Man-Eating Plant.
Ikeda seems to really enjoy writing Body Horror, considering how Hokuto turns into this.
- Then there's Kamiya Kanade, who claims that killing humans is just something he does to pass the time and clear his head, and envisions himself atop a mountain of corpses he personally killed.
Akuha cutting Moka's mother in half as well as her secret Yandere side for Moka.