There are some good times and not so good times to visit Japan!!! Read on!

Good Times:
Not as Good:
Cherry Blossom Time: The most beautiful time is during the cherry blossoms (sakura.) Unfortunately, it's hard to catch. The cherry blossoms are only really in bloom for one to two weeks, so you have to kind of guess when they'll be. End of March, starting of April is your best bet. Golden Week: The first week of May EVERYONE in Japan is travelling. If you come to Japan during Golden Week, get ready for long lines, and quickly booked transportation and hotels. If you are coming that week, make your reservations EARLY, EARLY, EARLY!!! But avoid this week if you can.
Spring. It's beautiful. Not as rainy or humid, and all the flowers are out and blooming. Second week of August. Same dealyo as above. Everyone is travellin', getting around is a mess.
Christmas: If you think we do up Christmas right in the States, come to Japan!! Seeing the Japanese take on Christmas is well worth it. You won't be homesick--everything is decked with lights and Christmas carols are everywhere! Rainy Season/Typhoon Season: This is more depending on where you're heading, but the rainy season in Japan is usually June-mid July. Of course it varies, and not every day is going to be rainy. But expect some serious humidity along the coast and in the Tokyo area!! Typhoon season is right around September.
Festivals: Pick a week, and you can find a festival somewhere. Try to plan your visit around one or two of them, if possible. It's a great way to experience some of the culture of Japan. In most areas, summer is hot and humid. Unfortunately, that's when most people have the time to come and visit. So just be prepared if you do, and plan accordingly.