Climate
Winter
Winter is a good time to go skiing or hot-spring hopping, but as some buildings lack central heating, it's often miserably cold indoors. Heading south to Okinawa provides some relief. There is usually heavy snow in Hokkaido and northeast Japan due to the cold wind blasts from Siberia. Note that the Pacific coast of Honshu (where most major cities are located) has milder winters than the Sea of Japan coast: it may be snowing in Kyoto while it is cloudy or sprinkling rain in Osaka, an hour away. Late winter also has the plum blossoms which precede the cherry blossoms.
Spring
Spring is one of the best times 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 (sakura) and is a time of revelry and festivals. For the southern half of the country, cherry blossom season typically starts towards the end of March and peaks in early April. The northern half has its season in mid to late April, up to Hokkaido which is in early May. Aside from the cherry blossoms, there is a lot more eye-candy afterwards, such as Japan's azaleas, roses, and wisteria.
Summer
Summer starts with a dreary rainy season (known as tsuyu or baiu) in June and turns into a steambath in July-August, with extreme humidity and the temperature heading as high as 35°C. Avoid, or head to northern Hokkaido or the mountains of Chubu and Tohoku to escape. The upside, though, is a slew of fireworks shows (花火大会 hanabi taikai) and festivals big and small.
Autumn
Autumn, starting in September, is also an excellent time to be in Japan. Temperatures and humidity become more tolerable, fair days are common and fall colors can be just as impressive as cherry blossoms. However, in early autumn typhoons often hit the southern parts of Japan and bring everything to a standstill. The ideal time for autumn colors for the southern half of the country is typically in the second half of November. Mountainous areas and those farther north have their's earlier.