Near the end of Ruby Quest, one of the most dangerous and insane mutants is found crying in a corner because Ace is coming.
BKCRMWDJVG of the Whateley Universe. When even a small part of it is let onto Earth, it causes insanity and terror and mindrape just by revealing its true appearance.
Atop the Fourth Wall: Lord Vyce. Interestingly, virtually no one except Vyce himself has heard of the far more dangerous Entity he was battling.
Less eldritchy, but Todd in the Shadows visibly sinks lower every time The Nostalgia Chick tries to get him to spend time with her. Considering some of the things she's done, his fear is very justified.
SCP-173 SCP Foundation a living sculpture that kills its victims when they break eye contact with it. What puts it firmly in this category, however, is that 682, the regenerating lizard that just doesn't die, and hates all life on earth, only yelped in what appeared to be terror and stared at it for hours when put in the same room, merely growing new eyes when they were shot out so 173 did its thing. When you scare the crap out of this thing, you know you're feared.
Among the Slaughterhouse Nine, there is one who inspires more dread than any other, even within their ranks: Gray Boy. When Jack decided to have all the past members cloned by a factor of nine each, Gray Boy was the sole exception. Bonesaw guesses that one Gray Boy is all Jack could hope to control.
Mario Brothers has King Koopa, who is portrayed as a terrifying, nigh-unstoppable villain.