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.

Japanican is a subsidiary of JTB and is a Tokyo Metropolitan Government Registered Travel Agency. It is a great site to get tour deals and to look for Japan related information on hotels, ryokan and accommodation in general.

Founded in 1990, The International Tourism Center of Japan (ITCJ) plans and conducts a variety of tourism-related businesses with Japan National Tourist Organization (JNTO).  They predominantly assist foreign tourists by providing wide-ranging information at the Tourist Information Centers (TICs) they operate at Narita International Airport and Kansai International Airport.

Highlighting Japan is an online magazine published once a month by the Japanese Government. If you are looking for Japanese tourism resources and general tourist information on Japan, this site is a goldmine.

Highlighting Japan has a lot of very informative articles which you can read online which provide a wealth of information from cutting edge technology, economics, politics, science, Japanese trends, education in Japan etc.

JNTO (Japan National Tourist Organization) is a Japanese government site which is great for finding useful tourism resources on Japan. They have information on online budget hotel reservations, regional guides, convention locations, festival information, seasonal attractions, museums and a vareity of very interesting in depth articles.

Discover Japan is a great site for finding Japan Tourism Resources. You can search tourist spots in Japan by choosing a keyword, an area or by a themed keyword. The tourism reources they provide focus on uncovering Japan treasures (i.e. places not commonly known to tourists).

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.