There are too many good ones to choose the best. Some of my favourites are Drunken Angel (a young Mifune, brooding, young, rebellious Yakuza), Rashomon (playing a bunch of different roles), The Hidden Fortress (great spear fight), The Bad Sleep Well (contemporary setting, about revenge, a tragedy), and Yojinbo. The great thing about him was that he played a distinctively different role in almost every film.
I heard recently that Holywood is to make yet another remake, this time of Drunken Angel.