Just got back a month ago. How long are you going for? We particularly enjoyed Nikko, Kyoto and Nara. I really wish we had more time for Kyoto-when we go back we will be visiting there again. Be prepared for it to be hot! Was getting warm at the end of April already. Travelling within Japan was fairly expensive, hotels were okay(business hotel-about $80 a night) but the Shikansen tickets were expensive (bullet train) I think we spent a few hundred each on those. We also went to Koyasan which was neat as it was small and not too touristy (is the birth place of buddhism in Japan) but it is sort of out of the way.
Buy a Pasmo-will make your life much easier, it is a reloadable card for the train, you just wave it in front of the gates and it deducts however much it needs to-way easier than tickets all the time.
If you go to Nikko stay in a Ryokan (traditional Japanese hotel) we stayed there and in a temple and it was some of the best food I have ever eaten-amazing. We had a lot of fun in Nikko, lots to see and small enough you can walk around. Stuff there though closes early. Ryokan for one night and the train tickets to Nikko were about $700 for the two of us but was amazing. Glad I went there. There is lake on the top of the moutain too that is kind of neat to walk around, big waterfall.
Lots to do in Tokyo too. I did get a little templed out though, temples and shrines are everywhere, and I mean everywhere.
Food is either hit or miss too, either really really good or very bad. I personally did not find food that expensive there but eat lots of beef before you go because there is not much of it there and what is there is not very good.
Oh, we also went to Enoshima, which is a day trip from Tokyo and really not too far, it was really neat also. It is out by the ocean and had a bunch of temples and eagles flying around. Was pretty neat being on the Ocean I though, I really liked it.