This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / VeggieTales
BAD BIRD!! BAD BIRD!!!
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.
Heck, almost all of Rumor Weed qualifies. Particularly the beginning, when the Rumor Weed is created. The gossiping woman in the window has arms and legs, not to mention a rather uncanny, human-like design. She instantly vanishes after that. Oh, and let's not forget the Rumor Weed's Slasher Smile when she faces the audience after her birth, accompanied by some very creepy music.
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.
The Nightmare Sequence at the beginning of The End of Silliness. Poor Larry... To be specific, the video opens with Larry distraught over the events of the "Cebu Song" and "His Cheeseburger", wherein "Silly Songs with Larry" is allegedly canceled. We see Larry having bad flashbacks by himself in a diner, represented by versions of "Cebu Song" and "His Cheeseburger" playing over top each other with the audio and video heavily distorted.
Speaking of "His Cheeseburger", that clown head is really creepy-looking, with many extreme closeups of it and its' big blue eyes staring directly at you!
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 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 VeggieTales 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.
"Easter Future" in "Easter Carol", a world without hope, is pretty terrifying since not only do we see Edmund/Junior's grave but it's all but stated that cops don't actually do their jobs because dying is too frightening a prospect.
Bob's character being trapped in a factory is a pretty frightening turn as well, especially given how panicked Larry's character sounds when he reports this.