For me it would be Princess Mononoke, which is also one of my favorite films, period. I really appreciate the maturity and nuance it brings to it's environmental themes, which have been done in many other films, but not as well.
I watch Miyazaki's movies every now and again, and the one that I probably have seen the most is Castle in the Sky. I don't know why, exactly. Close contenders with that is Howl's Moving Castle and Porco Rosso.