The Secret of NIMH/Fridge

Fridge Brilliance

 * The reason Timmy has to be the hero in the sequel is that if Martin was the hero, Timmy wouldn't care enough to do a Face Heel Turn, breaking the Self-Fulfilling Prophecy. Of course, that makes Timmy's hero status EVEN MORE arbitrary.
 * Why Mrs. Brisby and Shrew are able to act like humans even though they weren't experimented on. When Mrs. Brisby went to see Nicodemus, she mentioned among most things that Jonathan taught her how to read. So odds are Jonathan also taught her how to do other human like traits such as housekeeping. It also shows that the animals have the capacity to think and learn like humans without the aid of experiments, as Jeremy was able to function enough to wear disguises.

Fridge Horror

 * The much disavowed sequel to The Secret of NIMH, The Secret of NIMH 2: Timmy to the Rescue has one particularly disturbing Fridge Horror moment. . It is not scary as a little kid, but once you know some history, several very unpleasant instances of human experimentation come to mind.
 * There's also a "Quickthaw" variant of the same scene: Imagine showing up for work in NIMH one day and several other scientists who may have been your colleagues capture and forcibly experiment upon you. When it's all said and done you are left as a canine in a human's body. And it isn't a whole lot better to think they might have volunteered for this experiment.
 * What if they made you a man in a dog's body?
 * Another example of a "Freeze-by-Time" one, in which you have to know a bit about animal behavior, is especially terrifying; animals, even domestic species, don't just go to people naturally. You have to condition and imprint and handle these animals, especially at a young age, before they look up to a human as someone to trust. Wild animals will avoid people, even if they have food. Most people think the alley cats from before were just that; stray cats. But, their trust of a human, and their willingness to follow him, can only mean one thing; these were once someone's pets, and they're experimenting on them. Not only that, but the fact that all you see to try to bring in cats was a bowl of food for them, and they weren't wearing gloves in case the cats scratched them, meant that very docile, pet cats, were what they were after. After all, they've been studying mental health, and this has been known for a while.
 * Remember how terrifying the scene is when Mrs. Brisby tries to drug Dragon? Now imagine it from her perspective: the two she knows have done it have enhanced intelligence over her, but Mr. Ages broke a leg trying it, and Jonathan, her beloved husband, died in the attempt. She's just a mouse... oh, and one whose failure would mean a horrible death for her son, while orphaning her remaining children.

Fridge Logic

 * Why was Jenner so determined to keep the rats from leaving anyway? You could argue that he desperately wanted to rule, but he could've ruled somewhere else too, not to mention that he knew NIMH was coming and would likely take him back to a life of imprisonment or death.
 * The reason Jenner didn't want to leave is because he's strongly against "The Plan" . He even, thinking it would put a permanent stop to "The Plan." Additionally,  . Add to that Jenner didn't come off as particularly stable a being.
 * Also, Jenner was willing to fight NIMH. If he had stolen the Stone, it isn't hard to imagine he would have won.
 * Not really. The Stone doesn't work for everyone. Courage of the heart is what activates it, something Brisby demonstrated throughout the entire journey to save her children. Even if Jenner killed Brisby and taken the stone, he wouldn't stand a chance against NIMH because he wouldn't know how it worked.