The tractor scene is very unnerving, with the heavily rotoscoped tractor slowly creeping through the field and deliberately clashing with the rest of the film's Disneyesque style. The fact that the whole thing takes place from the perspective of the animals, with The Shrew running through the field screaming "THE PLOW IS HERE!!" turns a simple farming job into Armageddon.
Jenner, for his actions, demeanor, and utter ruthlessness in getting what he wants. In the scene where he tells Sullivan about his plan to kill Nicodemus, he tells about how the Brisby house will "crush his bones" while pulling off a Nightmare Face. When asked what to do about Justin, Jenner's response is an echoing "Leave him to me... to me... to me..."
The Great Owl, although he's neutral at worst, is first depicted gorily crushing a spider, and looks quite dark and intimidating even in comparison to the rest of the film.
The spider that he crushes is far scarier.
Dragon, the farmer's massive cat. It's much worse than it sounds.
The sequence describing the rats' experience at NIMH. Starts off with sad imagery of animals in too-small cages, then they show a rat being injected with God-knows-what and the Disney Acid Sequence begins.
The expression on Jenner's face as he is killed by the knife Sullivan threw into his back.