Japan National Tourist Organization
You couldn't find any better than this. Especially the "Practical Travel Guides".

Japan Guide
I found this especially useful too. Clean-cut layout and intuitive navigation. The section which helps you plan your itinerary was particularly useful for me.

Rising Sun Directory

Japan Zone

My Trip
English version is available as well, but choice of places to stay is most certainly not as wide as in the Japanese version.

Jalan.net

Yadoplaza
In English. Relatively good variety to choose from. Japanese version also available, of course, but I found the English section sufficient.