As time goes on, I’ll be updating a collection of sites that will save you time when planning your trip to Japan.
Here is what I recommend:

To research about Japan: Web-Japan

To learn about different places in Japan:  Japan National Tourist Organization or Japan Reference.

Looking for hotels:  Rakuten Travel
Jalan.net-Japanese only
Ikyu.com
Jal.com
Travel to and from Japan: Jal.com
Checking flights and routings:  JAL.com Orbitz.com
Buying a ticket:  Jal.com or a local travel agency. (Tip: Find out if that Travel Agency      is a wholesaler for JAL or which ever airline company that you want to use)

Traveling in Japan: JR / Japan Railpass

Reading Japanese websites: hiragana.jp/en
Rikaichan-an interactive tool for Firefox