What about Fritz the Cat? ;) As far as I can remember, it was the first X-rated cartoon. Which made it extra-special in my eyes.
I actually loved The Iron Giant, and was very upset at Warner Brothers for them not giving it more attention or the marketing that it needed. It didn't do well at the box office, because no one knew about it. WB Feature really worked hard on that film, and I don't blame Brad Bird one bit for moving on to Pixar. He belongs somewhere where he will be appreciated.
I don't know if this counts as a movie per se, but I loved The Animatrix. I thought it was very well done and really expanded upon the Matrix universe.
In terms of anime, Ghost in the Shell is pretty damn amazing, and so is Perfect Blue.
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