Not sure if you already know, but you seem to like
Hayao Miyazaki films(Spirited Away, Whisper of the Heart), so I guess you've seen most of them? Nausicaa, Princess Mononoke, and Kiki's Delivery Service are some of my favorites =03.
Perfect Blue deserves a mention, directed by Satoshi Kon, who also did Tokyo Godfathers, so that'll probably be up your alley. It has a darker theme though
.
You might like
The Girl Who Leapt Through Time as well.