I haven't been to Japan, but I've have a few friends who have. The one thing they all have recommended to me (and I guess I'm passing on their recommendation) is to go to an authetic Japanese Temple and there are even houses that do the whole traditional Japanese thing like Green Tea Ceremonies. I've heard the countryside is quite beautiful. Harajuku (the suburb in Tokyo) is also an interesting place to visit- that's where the teenagers and young Japanese people dress up in some weird and wonderful fashions.
Also it would be handy to know a couple of Japanese phrases to get around. That's all I've heard about Japan anyway. And yes, Disneyland and DisneySea are a must (and there is that Indy and the Temple of the Crystal Skull ride at DisneySea).