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Donald Duck's breakdown in the "Mickey and the Beanstalk" segment. Surrounded by death, no possible source of food beyond the bit of bread and beans, and absolutely no hope. He freaks out and tries to eat his plate and silverware. Mickey and Goofy almost have to strangle him to get him to stop. Then he sees the cow they own and goes Ax-Crazy on it in an attempt to kill it. The scariest things about these scenes weren't Donald suddenly going mad or his murderous impulses, but the realism of said portrayal. Donald's insanity is the result of desperate starvation due to an extreme famine, and it's a common fact that desperation due to near-death situations usually brings out the most violent, ugliest sides of human nature.
The last 15 minutes of the Sleepy Hollow segment is all about the mental shock-and-trauma. Not only do we have Brom Bones's ultra-creepy song to put Ichabod on edge, Icky then has to trek home through a Forrest O'Doom where everything seems to want to kill him. And then something wants to kill him. And it does. "And some don't even wear their skin!!"
Cruella De Vil has some pretty scary moments. Maybe the worst is when she drives right at the camera with this face◊, but there's also the scene where the dogs are hiding in an old shed and she suddenly drives past really slowly, glaring in the window. Turned Up to Eleven when she comes back shortly thereafter, going the other way.
Pongo and Perdita's attack on Horace and Jasper. It's supposed to be epic, but they look scary!
Jasper: What have we got here? A couple of spotted hyenas?
Mad Madam Mim. Her Villain Song and her duel with Merlin are both pretty unsettling. And if those weren't creepy enough, the part where Merlin wins the duel by turning into a virus would probably count.