I just watched this movie again and I'm still baffled by how the animators did the super mouse at the end. I am familiar with Bluth using old techniques but this one seems rather original, as he seemed to use it in All Dogs Go To Heaven during the car falling into the water and the satan part. Could anyone give any hints on how this was done?
Actually, I'm pretty sure I know how the Giant Mouse of Minsk was accomplished.
From what I can tell by looking at it, it wasn't drawn from scratch. I am guessing that they built and filmed a live-action model/puppet (notice that the head and mouth move), and then traced the footage to animation using rotoscope. I think the incredibly realistic-looking turnarounds of the Statue of Liberty at the end were done the same way.
If you look at the end credits of some Bluth films, you will see a listing for "model makers." I'm assuming that those credits were for these kinds of effects.