Ran, Rashomon, Yojimbo and Seven Samurai are the best Japanese films I have seen (and some of the best I have seen, period), closely followed by other Kurosawa works and other movies starring Toshiro Mifune. I also like the Lone Wolf and Cub-movies.
If I had to make just one pick, it would be Yojimbo. A very good and enjoyable film, just as good as "Fistful of Dollars" starring Clint Eastwood, the western that was based on Yojimbo. Great films