In Larry-Boy! And the Fib from Outer Space!, Junior's lies about breaking a plate end up getting him captured by a giant monster who proceeds to attack the city and destroy cars and buildings. Said monster also threatens to eat Junior and actually does try to eat Larry-Boy.
Larry-Boy! And the Rumor Weed! has a scene where Larry-Boy is in the Mother Weed's lair, without any way to contact Alfred. And then the Mother Weed shows up.
King George and the Ducky: King George sends Thomas to the Pie War over a rubber duck, causing Thomas to go insane. Even with knowing they're Animated Actors, seeing Larry of all people do something so awful and callous is unsettling, and Thomas being played by Junior pushes the whole thing uncomfortably into Child Soldiers territory.
Even though it's a Bowdlerisation, in Esther: The Girl Who Became Queen, the grim tickler that shows up to bring people to the Island of Perpetual Tickling is pretty disturbing, what with his way of appearing seemingly out of nowhere and the scary organ music playing in the background.
Fridge Horror: The "Island of Perpetual Tickling" mentioned in Esther is intended to be a G-rated version of the hangings in the original Bible story, but once you know that there have been at least ten recorded cases in Real Life of people dying of laughter, it doesn't take too long to realize that being banished there would be a very painful way to die.
The climax in "Rack Shack And Benny" when Mr.Nezzer sends them to the furnace for being "Bad Bunnies." Imagine what could happen to them if they didn't get saved.
It gets saved for a minor Incredibly Lame Pun Nezzer makes. Though still nightmarish, when out of context, it's pretty dang hilarious.
Worse still, eventhough it is seconds before he is redeemed after the boys are saved, Mr. Nezzer practically borders on the Moral Event Horizon after witnessing their plunge into the furnace with an Evil Laugh and some Evil Gloating to go with it. Contributing to the entry above on what would happen if Rack, Shack, and Benny didn't get saved from the flames, just imagine what kind of person Mr. Nezzer would have become after that. Definitely NOT the kind of boss you'd want to work for.
The Bad Apple from Larry-Boy and the Bad Apple has spider legs for a bottom half, and is generally creepy.
The Slap of No Return from Jonah A Veggie Tales Movie. Basically it's a giant club on a lever that smashes its victims like a bug. That they actually give a demonstration of how it works (with a thankfully non-sentient pumpkin) just made it even more disturbing.
The Pirates Who Dont Do Anything DVD includes a bonus scene where Mr Lunt's character experiments with a modified version of the time traveling device used in the movie. Choas ensues first with events repeating, Larry turning into a baby...Body Horror of the highest order...with some of the insane tranformations Larry, Lunt, and Pa Grape go through, it gets kinda hard to believe that this is an official scene made by Big Idea and not a Youtube Poop or something. See it here.