They had to change the name Frisby to Brisby due to concerns about the Frisbee trademark.
The movie makes the story more "creepy" I suppose. The NIMH experminetation isn't waved off like it is in the books. If I remember right the book has the Rats talk about how the syringes didn't even hurt and that they were treated well. The movie depiction of NIMH(as brief as it is) is more like an animal test lab.
The plow actually starts in the movie and is a small conflict towards the start that spurs Mrs. Brisby into seeking help. She and Auntie Shrew disable the tractor.
Bluth added a lot of straight up magic which actually ends up working really well. Nicodemus isn't just one of the smartest of the Rats, he's straight up a wizard to. He also dies towards the end.
Jenner is alive in the movie, instead of dead before the events of the story like in the book. He's great and gives the story a much-needed antagonistic force.
They cut out/condensed the backstory for the Rats. We still do see their backstory but like >>113613150
said we don't really see anything between their escape and them being on the farm. The movie just starts with them already having established an intricate, highly-advanced society in the Rose bush on the farm