Here are some links that me and Gav found, when we were in search for information for out trip

Travel

www.statravel.com : STA Travel, this is a great site for student discount fares, it has nearly everything you need to travel around the world as a student or young person. However, you do need to join up as a member and there is an age limit, available only to person's under age 26 and students. 

www.jnto.go.jp : Japan National Tourist Organisation, this site has lots of information about traveling to Japan. It contains info on places to eat, places to stay, guide to Japan, maps and general info on being a tourist in Japan.

www.tcvb.or.jp : YES! TOKYO, this is another tourist information site, but it's concentrated more on just Tokyo. It has travel guides, maps and lots of other bits of info on being a tourist in Tokyo. Very useful if you just going to Tokyo.

Places To Stay

www.japanhotel.net : Japan Hotel Network, this is a great site to help you find a hotel in Japan. They have an extensive database of nearly every hotel for every part of Japan. They also have a good amount of info for every hotel, ranging from room rates to how to get there. With an easy to use search, there isn't another site that can really beat this.

Information

www.japanreference.com : Japanreference.com, this site is like the Yahoo! search, but it's completely dedicated to any info on Japan or Japanese culture, ranging from Tradition Tea Ceremonies to Japanese Rock.

www.realjapan.net : Real Japan, this is site written by a Japanese girl (Alisha Senada) who has lived in US, is mainly about what's life like in Japan and Japanese entertainment (TV and music). It does have a bit on how to speak Japanese slang and how to be Japanese.

www.japanforever.net : Japan Forever, this is a site dedicated to Japanese culture (the fun side of it), it has lots of misc. info. It does have a small guide to Tokyo, it's not much, but it does have useful information.

Currency

www.oanda.com : Well, this is a good currency converter, very easy to use.

Misc