Anything by Miyazaki -
Grave of the Fireflies and
Spirited Away are at the top of my list.
Castle in the Sky has especially mind-bending visuals.
Most of the Japanese movies I like are not sf/f, go figure...
After Life - oddball movie about life after death, but not in an sf/f way.
Departures - another excellent movie about death.
Kwaidan - four stories based on Japanese ghost stories, very cool movie (and thanks for reminding me of this, I'm due for a rewatch.)
The Twilight Samurai and
The Blind Swordsman: Zatoichi - two very different take on the genre.
Tampopo - really different.
Akira Kurasawa's Dreams - really really different.
Ugetsu, Ikiru, Harakiri - intense human drama.
Hidden Fortress, Ran, Rashomon,
Seven Samurai,
Yojimbo - obvious suggestions, but just in case you haven't seen these already, they should be at the top of your list.