This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Jonny Quest: The Real Adventures
The nerve gas attack in "Escape to Questworld". You can see the agonizing look on the construction workers' faces as rigor mortis sets in.
The hunter getting mauled by a tiger in the episode "Manhattan Maneater". Seeing nothing but the tiger's claws only adds to the terror.
The greedy developer eaten alive by alligators in "Alligators and Okeechobee Vikings". Though it's offscreen, you can see the movements of the gators' heads as they rend the flesh asunder.
In "The Mummies of Malenque", a mad scientist and self-proclaimed descendant of the Malenque plans to infect the world with an ancient virus. However he gets a taste of his own medicine (well, disease) as his ancestors rise from their graves and give him a good whiff of the virus.
In "The Haunted Sonata", the climax includes the ghost of the original composer of the sonata, who was hidden in the wall of the basement after being pushed down the stairs and breaking her neck, come back to kill the greedy descendent of the man who killed her. She drags him into the wall by the neck and the wall reforms around them, sealing him inside with her red-eyed corpse.
"The Secret of the Moai" has Race and Dr. Quest de-evolved into ape-like animals in Quest World. That's freaky enough, but when they're removed from the computer, they still are mentally animals and run around, trying to attack their kids.
"In the Darkness of the Moon" features a very unlucky guy who, at the start of the episode, changes into a wolf in a way that sounds very unpleasant. He later saves Jonny from drowning and can talk, but he's clearly in pain and seems to still have something physically off about him, since the camera never shows him directly.