Few sites I found very useful when planning travel to Japan
1. Japan Guide – almost all information you need about Japan and a useful forum to ask questions/share.
2. Hyperdia – super useful on checking transportation in Japan including timetable and fares. I also have the apps one installed in my phone.
3. JNTO (Japan Nationa Tourism Organization) – useful interaction maps and itinerary suggestion.
4. Tokyo Metro – for Tokyo Subway Maps
One thing I did not find is a site that provides a good downloadable maps of Japan. Whereas I consider this very important on planning my trips. I need to know geographically the places to decide travel route (together with subway/train maps).
I did find what I was looking for in form of brochure, when I arrived in Japan in Tourist Information Center.
Hope this is useful for you who is going to exlplore Japan. Happy traveling!