I've been meaning to ask the same question, Uran-chama. I'm going in October and I see the travel agent next week.
![Smile :-)](./images/smilies/smile.gif)
Tokyo and Osaka are on my list at the moment.
Festival lists seem to be a great place to start because you can organise your travels around those schedules.
http://www.jnto.go.jp/eng/location/festivals/In Tokyo I'd like to see the city itself, Akihabara, and Pier 21 in Kodaira. Pier 21 is a video arcade I heard someone recommend in a Tetris video, which seems like a totally random thing to go and see, but I thought why not?
In Osaka there's the Tezuka Museum in the north-west (technically in Takarazuka I guess), and I'd like to see the Nara Deer Park in the east. I think the Tezuka Museum that closed was the one in Kyoto? The Osaka one is still open but it's closed on Wednesdays. I want to try out the bullet train too.
Beyond that I'm not sure what to visit. I'm told Hiroshima and Nagasaki are good if you want to travel that far down the coast, but I find the war stuff really upsetting. Kyoto sounds good because there's lots of historic things. I wouldn't mind seeing some rural stuff, cause I find old stories of feudal Japan more enthralling than the bright lights of Tokyo.