If you are coming to Japan, you should try to get the Japan In Your Pocket series of guidebooks. I’ve just spied one of them in my hostel and they’re great. A completely different style to your usual guidebooks, but very entertaining. The Today’s Japan one covers everything from how the trains work, through to transport and food. There are books on different areas of Japan, and different parts of the culture. I’ve found these books a bit too late, but think I’ll buy some of them as (more) personal souvenirs. I’m not sure how easy they will be to find elsewhere though – luckily the guy in the hostel has found a shop that should have them in Tokyo for me.
For train timetables a fantastic resource is the Hyperpedia Japan Rail Timetable online in English.
I’ll try to put more online links once I get home (!) next week.
A great resource: JNTO travel guides
http://www.jnto.go.jp/eng/location/rtg/index.html
I love their mapped out walks through different cities. Their maps are easy to read and great for printing.