Most of my favorites have already been said. :X But there are a few more I would recommend:
My absolute top recommendation would be
the Secret of NIMH. It was one of my favorite movies growing up and still is. For a movie made 30 years ago, the animation is quite impressive. The plot is a little dark but very captivating.
Also, watch
An American Tale if you haven't already. It has a nice message and the cutest main character. ^^
You said you didn't mind gore, so you won't have a problem watching
Watership Down.

Just be warned that it is VERY dark for a children's movie and it does feature a few humans.
And I might as well throw in
Once Upon a Forest.

I haven't watched it since I was very young, but I remember liking it.
lol I dunno why I chose so many mouse movies...
