I agree with Jihn Mace - Kyoto is not to be missed if you can fit it into your plans.
Do you have an idea of what where you’ll be going or are we starting from scratch here?
Couple random Ideas…
Tokyo
Disneyland: skip it, you can do that here (obvoius, I know).
Edo Castle is one thing you really need to see.
Ginza is cool to take a walk around at night but after a while it gets boring.
Some people will say you have to go to Tokyo Tower - again I’d skip it, it’s cool for like 10 minutes and then you’ll want to leave.
Try to hit a club, the nightclubs are a trip!
Kyoto
Kiyomizu-dera is spectacular. If you only visit one temple in Kyoto make it this one.
The Kyoto Handicraft Center will honestly blow your mind.
Go to Sanjūsangen-dō and make sure to see ther 1001 Buddhas (note: picture taking inside the hall is STRICTLY forbidden by guests, they’ll get very upset if you try, some guy tried it last time we were there).