Thought of the Day - The way to go
Just like in Europe you can get a rail pass (I know you can in the States too but why would you want to travel Amtrak all over the place). It was really a great deal. One round trip to Kyoto from Tokyo more than paid for the pass. All other travel was 'free'. Worked on a lot of the local subway lines too.
While I didn't get to travel extensively throughout Japan, this is definately the way to go. For ~$250 you could spend all week on the train going from one end to the other. (for reference, Tokyo - Kyoto roundtrip is about that much).