Jeremy may be dumb for a corvid, but he most definitely has their universal attraction to sparklies.
To a child, the weird images in the "our world began changing" sequence might look like they're supposed to be pain-induced hallucinations the rats were experiencing—just abstract nightmare images with no rhyme or reason. But those who understand more biology may notice that the twisty ladder-like structures are supposed to be DNA strands being disrupted, mutated...and as they changed, so did the way the rats viewed their world.
Some clips in this wiki describe the Great Owl as thematically a dragon. It makes sense; a giant flying beast that's both very dangerous and very wise in old age. Then there's the cobwebbing stuck to his wings and back. The webs are meant to make his normally feathered wings look like a western dragon's leathery wings.
In a brief line, Mrs. Brisby claims her children have learned to read faster than even her. Makes sense, since unlike her, half of their DNA comes from Jonathan.
Notice how Mrs. Brisby's cape is in very poor conditions while all of her children's clothes are all intact and relatively well-trimmed, especially Teresa's. A small detail, but it shows just how much Brisby puts her children's needs above her own.
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.
NIMH is a real world organization. Not just that, but what happened to the rats and mice was based on real-life experiments. They were controversial, but they existed.
More sad than horror, but Jeremy's "Miss Right" is no where to be found in the sequel, nor does she get so much as a mentioning, suggesting the two may no longer be together. She acted as Jeremy's one Bone Throwing in the first film, so it comes off a little saddening for the poor crow.
The male characters who play a significant role in Mrs. Brisby's ordeal in the film (save for Mr. Ages and Nicodemus) have names starting with "J". Jonathan, her husband. Jeremy the crow. Justin the guard captain. Jenner the Big Bad.