Smallville/Nightmare Fuel

With a show like the origins of Superman, the show has a lot of scary moments packed in there.

Season One

 * Metamorphosis: We see that the freak of the week villain skin comes off during a hot shower, with pieces of skin falling down like they were meat. And that's not the only thing wrong with him.
 * Just the whole aspect of Craving, where the power to suck the fat out of someone or an animal, in order to substance the Horror Hunger.

Season Two

 * Redux: If you thought Craving was horrific enough, this time the FOTW is able to suck the lifeforce out of someone and make them physically aged to old age. And that's not counting what happens when you see what the FOTW sees in the mirror.

Season Four

 * In Forever, the freak of the week has the power to freeze anyone he touches, almost like a wax figure. The scary part comes when whenever he freezes someone, they can still move their eyes and are so fragile, they break apart like the T-1000.

Season Five

 * Brainiac. Just about everything about him is Nightmare Fuel. The cold personality, the ruthless manipulation of everyone around him, the Squick-enducing ability to Mind Probe victims by thrusting liquid metal fingers into their eyes, the matter of fact way he talks about eradicating life...he's this trope personified.