This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Adventures of Jimmy Neutron: Boy Genius
"We'll be BACK!"
The episode when Evil Jimmy tricks Jimmy into thinking he's good, and creates a new world that's sapping reality from earth. Jimmy proceeds to reverse the process, killing every one of the billions of evil humans. He killed a species. That's genocide. And what's worse: If he didn't his entire planet would die.Pretty dark for a kids show.
Many of the evil duplicates of Jimmy's friends, family, and acquaintances are also shown to be highly disturbing. Evil Jimmy's parents are shown to be the most deranged as Evil Judy is shown gleefully dirtying her house while Evil Hugh laughs sadistically after recounting how he killed and mounted ducks on his wall after they begged for mercy.
"One of Us" can get surprisingly scary at times, especially when Jimmy finds himself alone among his friends-turned-mindless zombies. The ending's rather intimidating as well: as the grandmother boards the mothership, it seems like the episode will only end on a peculiar "WTF" note. Instead, she turns around, lifts her glasses to reveal completely black eyes, and says "WE'LL BE BACK." in a terrifyingly deep voice. And to matters worse she returned in a later episode.
And that episode reveals that she can shoot lasers from her eyes, which she uses to disable Goddard. And then there's the following comment she makes after Baby Eddie insults her.
Win, Lose, or Kaboom has the race between Jimmy's team and the team of brainy aliens. When it seems like they have made it to the finish line, they return to Retroville and are greeted by their parents with a celebration of their supposed victory. When they find some things off (like the ice cream tasting like sheet rock), the "parents" urged them to "Eat and Forget" repeatedly in an increasingly unsettling manner like zombies. It was all a dream implemented by the brainy aliens to distract them; the only way they could wake up is to fall into the void outside where they find out they are in the middle of nowhere. It could be worse to think about what would happen if the "parents" have captured the kids.
When one of the Needleheads is forced to eat a banana cream pie, his head explodes. His headless, burnt stalk is left wandering around comedically for the rest of the movie, but still very unsettling. It's presumed a Needlehead's head can grow back.
The animation in this show. Growing up in the early 2000s back when most cartoons used 2d animation, the style seemed creepy and off-putting to some children. Especially the Jimmy-Timmy Power Hours, where characters who had always lived in a 2d world suddenly became computer-generated big-headed kids.
Don't forget forget to mention Johnny Quasar, the first ever Jimmy Neutron short. It's much more deranged and creepy.
Jimmy being reduced to a gelatinous slab after running around too fast. His body will eventually re-stabilize into solid matter.
A candy that electrocutes your mouth if you eat it.
Even more disturbingly, this doesn't deter Sheen from continuing to eat the candy. In the final scene, he mentions smelling smoke, his face being numb and seeing blue from all the shocks he's getting from eating the candy.
The episode where the gang goes to Retroland to try to disprove a ghost myth, with different people showing up dressed as the ghost to try to scare them. At the end, the real ghost appears to Jimmy's parents.
The episode where Jimmy, Sheen and Carl have a sleepover with a machine that cranks out scary stories, pillows, and pizzas. The climax is when Carl accidentally creates a flesh-eating pizza that chases them around the house, and a pack of flesh eating pillow go after the parents. At the end after disaster seems to be averted, the pizza monster strikes back - "Haven't you ever heard of sequels?" Then it spirals into a series of nightmares from each of the characters. While most of them are funny, one ends when Carl tries to hide under the parents' bed, but gets stuck and is eaten by the pizzas. Yikes.
"The Evil Beneath" is actually full of this. The plot follows Jimmy and his friends investigating to find the reason behind the string of boats and planes that disappeared in an area of the sea known as the Bahama Quadrangle. When they get there, they find Dr. Sidney Moist, one of Jimmy's scientist role models and leading researcher in phyto-chemicals compounds thought long dead. Though he comes off as a silly and goofy weirdo who likes tap dancing, he ends up revealing that he's been kidnapping people who come to the Quadrangle to turn them into Algae-based manservants because of his own psychotic paranoia that newcomers were sent to spy on him. He's done this many times and would have successfully done it to Jimmy and his friends if not for Jimmy finding a way to overload the Algae Men and destroy Dr. Moist's lab. After they destroy the lab and think they solved the mystery, a dense fog appears out of nowhere with multiple pairs glowing red eyes inside the fog (implied to be evil porpoises based on the screeching from the fog) and Jimmy and the gang decide to leave the mystery unsolved before fleeing away in terror.
"Nightmare in Retroville", appropriately enough for a Halloween special, has plenty of this. Jimmy's monster machine that he created in an attempt to make his friends look like monsters for Halloween actually turned them into monsters, complete with bloodlust, by mutating their molecular structure on a subatomic level and altering their DNA. As such, both Carl and Sheen become bloodthirsty monsters, hell bent on killing or turning others into monsters themselves:
Carl cuts his finger, starts sucking on his blood and actually enjoying this (because he's just starting to become a real Dracula), much to Jimmy and Sheen's disgust and confusion.
Sheen the werewolf stalks Libby for some time before approaching her, which we can see from his creepy first person perspective.
While it's not shown on screen and we never see any bite marks, both boys actually end up biting Cindy and Libby. Before that happens, we can see Carl's mouth slowly approaching Cindy's neck, and Libby screams for her life (definitely not in a G-rated manner) once Sheen jumps onto her. You could imagine a Real Life sexual assault playing out similar to these two encounters.
The DNA Productions logo screen at the end of every episode doesn't help much. A theme music similar to an Ominous Music Box Tune plays, and then a 3-eyed monkey jumps out, looks at the screen, and says (in a weird, squeaky voice) "HI! I'M PAUL!" It can be slightly disturbing for some viewers.