Japanese are proud of their four seasons (and a surprising number believe the phenomenon is unique to Japan), but the discerning tourist should try to aim for two of them.
Spring is probably the best time of year to be in Japan. The temperatures are warm but not hot, there's not too much rain, and March-April brings the justly famous cherry blossoms and is a time of revelry and festivals. Just watch out for Golden Week (April 27 to May 6), the longest holiday of the year, when everybody travels and everything is booked full.
Summer starts with a dreary rainy season in June and turns into a steam bath in July-August, with extreme humidity and the temperature heading as high as 40C (90F). You may want to do as the Japanese do and head to northern Hokkaido or the mountains of Chubu and Tohoku to escape. O-Bon (mid-August), when everybody is on the road again, makes travel more difficult. August also starts the Japanese typhoon season. Be careful and always check the daily weather forecasts.
Autumn - Fall, starting in September, is a close second to spring. Temperatures become more tolerable, fair days are common and fall colors can be just as impressive as cherry blossoms.
Winter is a good time to go skiing or hot-spring hopping. December to February has very short days, 5:00 pm sunsets, and very cold temperatures, around 5 degrees Celsius (40 degrees Fahrenheit). If you are not one who enjoys winter it may be a good time to travel to warmer climates (Okinawa, Hong Kong, Bali, etc.). Also watch out for New Year’s (December 29 to January 3), the only days of the year when everything in the country shuts down.