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Nightmare Fuel: The Clue Finders
The Medusa rock with snakes coming out of her eyes in 3rd Grade.
Any given part of Goo Lagoon in 3rd Grade can be this to the squeamish, and kids tend to freak out at the extremely Beatles-inspired song.
Try "Do You Believe in Monsters?" in Numeria. The red and black animations are really good at looking creepy. Even worse, the song mentions Mathra taking mothers, but the lion getting carried off by Mathra in the animation looks like a cub.
The aliens in 5th Grade.
The Reveal that they eat brains, and that they've captured everyone you've met on the island (and countless other people who sailed near it) to that end. Including Leslie's grandfather, which you see in a Jump Scare with a Scare Chord no less.
Furthermore, where you try to access the map inside the ship, Laptrap says, "Sorry! But we are now, trapped, inside!"
Pericles Lear in The Incredible Toy Store Adventure!
Laptrap's Evil Twin in "The Mystery of Microsneezia". He's as cruel and violent as Laptrap is meek and gentle, kidnapped Joni's uncle and Laptrap, impersonated the latter and subjugated an entire island. And if it hadn't been for Leslie's bubblegum being a cure for the disease caused by the plants on the titular island, he would have won.