This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / All-Star Superman
Sure, Lois was suffering chemical paranoia at the time, but the events are scary when you think about it—especially Superman's stalker-esque super-speed entrance with the flowers while she is alone in the fortress surrounded by terminator faced robots. Also, right after, as Superman is explaining things, it's still pretty scary. When did he get Lois's measurements? He memorized her genetic code? Think about that a moment—a man with the power of a god has secretly got your measurements and memorized every line of your genetic code without your knowledge?
Secretly? Lois and Superman have known each other for years at this point and have had dozens and dozens of adventures together. It would be weirder if he didn't know these things.
The situation in "The Superman-Olsen War'" is so dangerous that even the Moment of Awesome of the comic is rife with Fridge Horror. Yes, Jimmy did manage to minimize the damage the Black-Kryptonite-infected Superman could do by becoming Doomsday, but that may only have been possible because the Black Kryptonite was inverting the powerful, intelligent person he normally is. After concluding the situation was serious enough to drop his no-kill rule, Superman did kill Doomsday in the main continuity, and the Black-Kryptonite Superman would have no such scruples...
The Bizarro invasion. Imagine a cube shaped world that eats other worlds, that emerges from a dimension beneath ours. The Bizarros themselves are especially creepy. Hordes of misshapen zombie-like duplicates screaming backwards nonsense, and when they touch someone, that person loses their face and BECOMES a Bizarro.
Steve Lombard (who's immune to them due to his steroid habit), a character who's largely a complete jerk, freaks out during the invasion, particularly when he has to toss a friend of his off the fifth floor of a building in self-defense after she turns. "Good God, I just threw her out a window..."
Steve probably saved them all.
Bizarro-Green Lantern's ring makes everything he doesn't think about real, except he can only think of everything. Isn't that terrifying, paradoxical, sad and mindblowing on so many levels at the same time?
One can get the impression that Bizarro-Green Lantern meant that he was too stupid to think of anything for his power ring to work. Your typical Bizarro speech is often the opposite of what the pale doppelgangers really mean to say, and their tendency to engage in Confusing Multiple Negatives can sometimes make it hard to understand exactly what they mean.
The intelligent Bizarro (aka Zibarro) Superman meets is doomed to live a life of being a super-intelligent, forward speaking man on a world full of screaming imbeciles who ENJOY living in trash heaps.
Immediately frightening, but even more so when you consider the implication: That Luthor can and does grow people who believe that exploding is their basic human right, and uses them just to accuse Superman of interfering with their rights if he stops them from killing themselves. A moral conundrum which even Superman could in practice only solve by helping the thing die.
Parasite in the animated adaptation. Even though there's no gore, his murder of guards is just chilling.
The comic book version, too. From the moment he enters onstage, a lamprey in a straight-jacket screaming obscenities at Luthor, to his final appearance, bursting like an overripe grape beneath Luthor's boot, the comic is pure nightmare-fuel.
Luthor only went to prison because he wanted to. The human authorities had absolutely no chance.