I've been a few times now, and there are loads of things to see.

Tokyo has some great things, Tokyo tower, Asakusa shrine, the skyscrapers of Shinjuku (go see the Park Hyatt from Lost in Translation and go for a drink in the skybar). Ginza for shopping. Harajuku for the weird teen fashion. And of course the imperial palace which tends to be restricted but is worth seeing.

But the best thing about Tokyo is just the atmosphere, everyone is friendly and will help out with directions. The other thing is, most youngters speak english if your Nihongo isn't what it might be, but they READ English even better, so don't be afraid to write things down for them if you get really stuck.

Kyoto is a LOT more peaceful, the railway station there is amazing, you need to explore that and go to the rooftop garden - prefereably at night

Osaka the main thing is the Five building - it's like a mall but there's a ferris wheel on top definately worth going on.

A good guide book is all you'll need though, once you've worked out the train system, it's great

Enjoy.