I still like Mononoke. It was a little ham-fisted, but so was Nausicaa, and I liked Mononoke's rather low-key resolution over the messianic EVERYBODY GETS A CAR ending of Nausicaa. (Then again, I always liked the Nausicaa manga better.)
My personal favorite is probably still Cagliostro, though, because even if they amped up Lupin's moralfag aspects, it's still just a charming movie all-around.
That reminds me, I need to watch Spirited Away again sometime.