Wall-E - I'll keep nominating it until we see it.
Titan A.E. - Proto Firefly in a way, Joss Whedon was one of the writers and took a number of ideas from this movie to make the show. Also quite famously screwed over by Fox like Disney did with Treasure Planet, how dueling movies can go horribly wrong.
The Iron Giant - One of the best animated movies ever that almost no one saw when it originally came out, thanks a lot Warner Bros.
Who Framed Roger Rabbit - Cheating a bit since is a mix of actual humans and cartoon characters but is amazing and the special effects still hold up 30 years later.
I went with movies that maybe people haven't seen instead of the renaissance 90's era that most of us have.