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.