Here is a list of my personal favorite films from Japan (including co-productions).

Rated 10/10
Rashomon (Kurosawa, 1950)
Ikiru (Kurosawa, 1952)
Tokyo Story (Ozu, 1953)
Ugetsu Monagatari (Mizoguchi, 1953)
Seven Samurai (Kurosawa, 1954)

Rated 9/10
I Was Born, But… (Ozu, 1932)
Early Summer (Ozu, 1951)
Spirited Away (Miyazaki, 2001)

Rated 8/10
Throne of Blood (Kurosawa, 1957)
Floating Weeds (Ozu, 1959)
Yojimbo (Kurosawa, 1961)
Tora! Tora! Tora! (Fleischer & Fukasuku, 1970) (US/Japan)
Ran (Kurosawa, 1985)
Mishima: A Life in Four Chapters (Schrader, 1985) (US/Japan)
Tampopo (Itami, 1985)
Shall We Dance? (Suo, 1996)
Princess Mononoke (Miyazaki, 1997)