Its a really amazing place, as others have mentioned like nowhere else really.
Couple of tips, I know we, as tourists, shouldn't necessarily expect it; but don't underestimate how little English the people there speak. Hotel staff etc will probably be fine, but if you're out and about looking for directions to a place, the police (etc) likely won't speak a word.
Secondly, depending on the time of year you go, it could be very humid. I went in July, last time, and honestly, I wanted to spend most of my time on the subway system. That reminds me, avoid rush hour, its hell.
In the evening, I think Tokyo is at its most interesting. Street stalls pop up selling all sorts of crap, yaki tori stands pop up. I know people some times worry about eating street food, in my experience, street food in Japan is excellent, and won't leave you in the bathroom for the next 24 hours.
Kyoto is also very fascinating, definitely go.
If you get the chance, I'd go to Hiroshima. There is of course, the obligatory bomb museum; it is very sobering, however.
There is also a lot of other stuff to do, great food (try the Hiroshima Okonomiyaki).
Last time I went I climbed mount Fuji. Again if you get the chance, its well worth a visit.
