CIA - You can find general information here.
http://www.cia.gov/cia/publications/factbook/geos/ja/html
Japan Information Network - You can find information on the Japanese government (Parliament, Supreme Court, etc.)
http://www.jinjapan.org
Kids Web Japan - This site is really cute and geared toward 10-14 year olds, but it's a great source never-the-less. With graphics and sound bites, it has a plethora of information on Japan.
http://web-japan.org/kidsweb
News Information:
Japan Times - This site has the latest news of Japan, including entertainment, politics, etc.
http://www.japantimes.co.jp
Japan Today - This is another site that give the latest news of Japan.
http://www.japantoday.com
History and Travel Information:
Japan Guide - This site gives information on living and traveling in Japan. The site has interesting pieces about specific festivals in different regions in Japan. It also has a section on the history of Japan.
http://www.japan-guide.com
Japan National Tourist Organization - Like the site above, it gives information on living and traveling in Japan. However, it is run by the Japanese government. It's VERY easy to navigate!
http://www.jnto.go.jp
Language Information:
Download Japanese Fonts - I know that these fonts will download, but I don't know if they work the best. But hey, they're free.
http://www.learnjapanesefree.com/japanese-download.html
Do You Want to Learn Japanese? - This is a cute site with some stories that are written in Kanji, Hiragana, Roma-ji, and translated into English.
http://www.ifi.unizh.ch/ailab/people/thomas/erina/kana-romaji.html
Japanese Writing Tutor - This is an awesome site with practicing the letters! This site teaches the letters for hiragana, katakana, and basic kanji with correct stroke orders for each. It is VERY easy to use!
http://members.aol.com/writejapan/index.htm#write
Hiragana Game - A game to practice your Hiragana skills!
http://www.csus.edu/indiv/s/sheaa/projects/hiragana.html
Katakana Game - A game to practice your Katakana skills!
http://www.csus.edu/indiv/s/sheaa/projects/katakana.html
The Kanji SITE - This site helps in introducing the beginning kanji characters. It also has quick lessons on Hiragana and Katakana characters.
http://www.kanjisite.com
Practicing Giving Directions - This site has sound bites and graphics to show directions. You may practice giving directions with the sound bites! There are some vocab words on this site, as well.
http://www.sabotenweb.com/classes/mapex3
Japanese Text Initiative - This site by the University of Virginia Library, has a great collection of Japanese text available online. You can look up text by title or author. Most are translated already, but some are not and would be helpful in practicing reading in Japanese. Very Advanced!
http://etext.lib.virginia.edu/japanese/texts/index.html
Beatrix Potter's Children's Stories in Japanese - Oh! So Cute!
http://wiredforbooks.org/kids.htm
Japanese Children's DoCoMo - This site is so awesome! It has a great library of Japanese stories that you can read and listen to! It's all in Japanese, so I suggest upper levels to check it out!!!
http://www.digital-lib.nttdocomo.co.jp/kikakuten/index.html
Mangarama Collection - This site has a collection of Japanese Stories including audio clips. A little on the advanced side.
http://www.ak.cradle.titech.ac.jp/Rise/index.htm
For everything else ... Google it!
http://www.google.com