They have categorized the info by region, by temples, by natural beauty, by culture, or you can go with the general info, clicking the Japan Map. It is an extremely well-designed website.
Strongly suggest you get a JR Pass (Japan Rail Pass) - it can only be obtained OUTSIDE Japan - a true bargain for visitors - it allows unlimited train travel including Shankensan, the trip between Tokyo and Osaka via Shankensan, would easily = the cost of a 7day Pass.
The great part of the pass is, it only starts ticking the day you activate it. You can activate it at any JR station where it has service window. Tokyo and Kansai airport both have JR customer service offices where you can activate the pass and book your trains (not necessary, but if you intend to take nighttrain, it is advisable to prebook).
There is a Hongkong based Chinese website full of info about self-guided trips to Japan. I dont have the link now, but you probably can google it.