I have to admit, there's a variety of great anime movies, even outside of my favorite anime director: Hayao Miyazaki. But, I don't think it's possible for me to name just one. Metropolis is one of the best ones I've ever seen. I like how it's inspired and uses ideas from the late Osamu Tezuka.
Another one that's high on my list is My Neighbors the Yamadas. It was made in Studio Ghibli: The same studio that handled most of the Miyazaki movies. Despite the questionable, simple comic strip-style of animation, Isao Takahata brings the characters to life.