This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Young Justice: Darkness Falls
The way that this version of Doomsday is created is rather terrifying. Not to mention they describe him as being more muscled than Bane, Mammoth or Blockbuster.
Despite the Forgone Conclusion, Supergirl is rather scary as a fury. Brutal, fast, and relentless. And given that she's a full blood kryptonian, she's able to lay Conner flat during their fight.
Ghosts is a halloween episode, but by far the scariest part of the episode is when Jason Todd takes Nightwing prisoner, and acts all unhinged putting him through a Joker Jury.
The Watchtower attack. The Parademons and Suicide Jockeys, with both the element of surprise and their first encounter actually manage to give 18 different heroes a hard time including Dr. Fate and a Green Lantern, who both have notorious Story-Breaker Power.
The Vacuum of space is really creepy in how it nearly killed several heroes.
Cyborg's first appearances are rather unnerving with him being almost like The Juggernaut hunting down Raven and taking down Beast Boy.
The Bad Future gives us two bad guys that are really scary.
The Supermartian: the future son of Conner and M'gann, who effortlessly takes out over half of the team from the future.
The paratroll. The biggest and meanest of all the genomorphs of the future, and an Elite Mook without mercy.
The No-Holds-Barred Beatdown that Doomsday gives Superboy and Superman. You actually see very little of it, but it's clear from it that very little actually slowed down the beast.
Darkseid's surprise killing of Vandal Savage. And just like that, the former menace who was a cornerstone of The Light was eliminated with hardly a second thought.
Klarion's Evil Plan for defeating Dr. Fate. Not only did he have some rather forward thinking, but his evil laugh to set up for the act is rather unnerving.
Whatever Darkseid did to Kaliback in this universe. It's so awful that nobody on apokalips wants to talk about what happened to him.