The National Art Center, Tokyo is one of the newest museums in town, it opened three years ago. The temporary exhibitions are usually pretty good; however the museum is worth the visit simply to enjoy the interior architecture of the building. The National Art Center, Tokyo is located in Roppongi near Tokyo Midtown; you can find here a map in English.
One of the things that I like the most in the building is the cafeteria. One part of the cafeteria is on the top of a mug-shaped structure, and the rest of the cafeteria is below around the structure.