* Does anyone remember the episode when Evil Jimmy [[spoiler:tricks Jimmy into thinking he's good, and creates a new world that's sapping reality from earth]]? Jimmy proceeds to [[spoiler:reverse the process, killing every one of the billions of evil humans. He killed a species. That's xenocide.]]
** Evil Jimmy was planning on doing the exact same thing.
* "One of Us". Especially the ending. 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 [[BlackEyesOfEvil completely black eyes]], and says "WE'LL BE BACK." in a [[EvilSoundsDeep 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.
-->'''Grandma Taters''': I could just eat you up! '''''[[BlackEyesOfEvil ANd mAyBE]] [[EvilSoundsDeep I WilL]]!'''''
-->''Eddie understandably [[BringMeMyBrownPants poops himself]]''
* The giant spider in "Stranded!"
* The Nanobots proceeding to delete everyone from existence due to them being "flawed". If Jimmy hadn't intervened before they hit the "empty recycle bin" option...
* "Sheen's Brain" where Sheen's head [[BodyHorror eventually gets so big it takes over his body]].
* ''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. [[spoiler: 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 Twonkies.
* The animation in this show. I know that doesn't make as much sense now, but 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.