Thanks for the ringing endorsement!
By the way, here's a link to the thread on Japanese railways...
Actually, I've been looking around for some other sites that may be of use to you. The two things you will want to know up front, before you go, talk to a travel agent and see if you can get the Japan Rail Pass, you pay a bunch of cash up front, but it gives you unlimited access on any train on the Japan Railways (JR) system for a few days (any train anywhere... on JR)... from the locals to the Shinkansen ("bullet trains"). The other is the Seshin Ju Hatchi Kippu (SEH-shen JUU HA-chi KEY-pooh), or "Number 18 ticket," which costs about 150 bucks and gives you unlimited rides on any JR local, rapid or limited express for five days, which you can stretch out over a month or so after purchasing said ticket).
I used the "18 ticket" quite a bit and would reccomend it if you don't mind riding the train all day and making a few transfers along the way.
If you're just going to hit the major tourist spots, then just remember that the Tokaido sen (sen = line) is the major rail line between Tokyo and Osaka (which will also take you to Kyoto and Kobe). From Osaka you can get to Hiroshima and on to Nagasaki...
Tokyo... I have a guidebook a Japanese friend of mine gave me that has all the major lines in Tokyo listed - JR, private and subway lines - and also points out transit lines. He also gave me a guidebook on all the free attractions one can see in Tokyo (like the Toyta super showroom in Ikebukero ward, it has all the latest Toyota vehicles on display on 5 floors). I would reccomend you get both (let me do some digging to find the authors, ISBN numbers, etc.). Otherwise, the Yamanote (green) line is the Tokyo equivilent of the Chicago "loop" (it's a circular route around Tokyo like the "L's" loop around Chi-town) the Chuo line (orange) is the rapid train between Tokyo (Marunouchi) station and Shinjuku while the Sobu Chuo line (yellow) is the local train (third stop on that and the Yamanote line is Akihabara... land of electronics and anime).
But I can't really tell you much more at the moment. How far west or north do you plan on going? I can get you more info. if you can give me your general "game plan."