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.
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.