Michitravel is a travel agent that adds a personalized touch. They organize tours which cater to very individual needs to ensure you get the most out of your trip to Japan.  They have a great list of sample travel itineraries you can check out on their site.

Japan-guide.com is a comprehensive travel and living guide for Japan.You can also reserve hotel rooms directly from their site.

Japan National Tourist Organization is a Japanese government site which provides information for online budget hotel reservations, regional guides, convention locations, museums and more.

Japanvisitor.com has a wealth of information on Japan. In particular, they have a lot of in-depth articles on places to visit in Japan, segregated by region.