* The sound effects and incidental music, in combination with the DerangedAnimation.
* The screaming [[MonsterClown clown]] with the spinning head.
* Those fits the Chief Blue Meanie went into when stressed.
* The Dreadful Flying Glove. Most of the other meanies are that wacky, crazy type of evil, but the Glove is just pure, unfettered evil.
** Especially with that deep, terrifying laugh of his. Brrr...
* The Sea of Monsters, with all the multicolored, smiling creatures and strange noises were just so unsettling.
* The "Sea of Time" is sort of creepy for those afraid of mortality and aging.
* The weird maths equations, soundwave diagrams (the only live-action effects within the movie itself), and Creator/AndyWarhol-esque portraits of the Beatles floating in the Sea of Science, along with George's creepy, passive-aggressive "Only A Northern Song", make for one of the most ''inexplicably'' disturbing moments in the film.
* Jeremy. In his entirety. Every single moment. Always.
** [[UglyCute Or maybe not.]]
* When the boss Meanie raked his claws across his face and said "O-BLUUUUUUUUUUE-terate them!"
* The Beatles' home. Highlights being those that run up and down the corridors when nobody is about and the jump moment with King Kong.
* The fate of the conquered Pepperlanders. They seem to be frozen and senseless, but then we see a few of them [[AndIMustScream shedding tears]], or trying to move only to get even more forcibly put down.