For the most up to date list check out
http://vcejapanese.net/links/Top
http://lang-8.com/http://www.alc.co.jp/index.htmhttp://rikaichan.mozdev.org/http://nihongo-e-na.com/eng/Language Exchange
http://lang-8.com/ - HIGHLY RECOMMENDED
This is one of those "language exchange" sites, primarily for native Japanese and English speakers. Essentially you can write Japanese "journals" (but in reality you can just put practice essays), and native Japanese people, living in Japan will correct it for you. This site is quite active, so it's very likely you will get corrections quite promptly. In turn you can also correct Japanese people's English journals.
http://www.language-exchanges.org/http://www.mylanguageexchange.com/Grammar Resources
http://www.guidetojapanese.org/The Ultimate grammar guide (Written by a Korean, it must be good). Covers a lot of VCE Grammar, as well as post VCE grammar.
http://www.jgram.org/Not quite as well written as above, but still good. Community written so it covers more but may not be as reliable (like Wikipedia)
http://homepage3.nifty.com/i-yasu/bk-les.htmGrammar explanations in Japanese
Japanese learning Podcasts
http://www.japanesepod101.com/Regularly updated podcasts for various levels. If you have an iPod, just add the feed to iTunes. To access other resources (PDFs, "Learning Centre" on the site you have to pay a sizeable amount > <. Lower Intermediate is approximately VCE Level, Upper Intermediate is a bit harder than VCE, and the Advanced Audio Blog is quite difficult (JLPT2/1). There are also other side series that may be of interest
Dictionaries/Translation
English -> Japanese, Japanese -> English dictionaries
http://www.alc.co.jp/index.htm - HIGHLY RECOMMENDED
English to Japanese dictionary, which provides an array of examples.
http://www.csse.monash.edu.au/~jwb/cgi-bin/wwwjdic.cgi?1COne of the most prevalent dictionaries on the Internet, and is the basis for many web apps. If you have an iPhone/iPod touch there's an app called Kotoba which includes this dictionary
http://www.jisho.org/Uses the WWWjdic database, but is more user friendly, and also has way more sample sentences
Japanese -> Japanese dictionaries
http://dictionary.goo.ne.jp/http://www.sanseido.net/http://kotobank.jp/ - HIGHLY RECOMMENDED
Translation
http://translate.google.com/#Primary Sources
News Sites
(Rikai-chan or equivalent is recommended when reading these sites)
http://www.fnn-news.com/Japanese News with videos
http://www.yomiuri.co.jp/http://www.tv-asahi.co.jp/ann/news/web/index.htmlhttp://www.nhk.or.jp/http://news.tbs.co.jp/http://www.asahi.com/Web Portals
http://www.yahoo.co.jp/Number 1 visited site in Japan.
http://www.goo.ne.jp/Blog Portals
http://ameblo.jp/http://blogs.yahoo.co.jp/Audio
http://fantajikan.tea-nifty.com/blog/Japanese children books! (audio). Can be added as a feed to iTunes
http://how-to-learn-any-language.com/forum/forum_posts.asp?TID=6241&PN=1&TPN=1An extensive list of Japanese e-books
Kanji Resources
http://rikaichan.mozdev.org/ - HIGHLY RECOMMENDED
The ULTIMATE Firefox add-in. Gives popup readings/meanings for all Kanji. A must have.
http://www.jlpt-kanji.com/Flashcards for Kanji organized by JLPT level (Can be printed).
http://www.kanjisite.com/http://www.popjisyo.com/WebHint/Portal_e.aspxA website which provides pop up readings of hiragana, katakana and kanji. It's much like Altavista's Babel or Google Translator. Except it's better. It supports Japanese, Chinese and Korean.
http://nihongo.j-talk.com/parser/A Kanji to hiragana converter. Can be used for individual words, sentences, or whole web pages with little popup furigana (which may or may not work
http://www.rikai.com/perl/Home.plSame as above, but I find it isn't quite as reliable.
http://www.yamasa.cc/members/ocjs/kanjidic.nsf/SearchKanji3?OpenFormPro Kanji Dictionary that has readings, meanings, and even stroke order animations
http://japanese.about.com/library/weekly/aa070101a.htmLearn about Radicals, which may help you memorize Kanji more easily.
http://www.csus.edu/indiv/s/sheaa/projects/genki/kanji_main.htmlKanji worksheets designed for the Genki series of textbooks, but can be used without them.
Learning courses/tools
http://ichi2.net/anki/A highly advanced flashcard program. I would recommend creating your own flashcard decks from texts you are reading, rather than grinding premade decks which have little context.
http://iknow.jp/An advanced online flashcard like system
http://www.japaneseclass.jp/index.phpA Japanese vocab MMORPG kind of thing.
http://nihongoup.com/various games and courses to learn Japanese
http://kanjialive.lib.uchicago.edu/tool to learn Kanji
http://mykikitori.com/index.htmlvarious listening exercises
http://anime-manga.jp/index.html various fun games to learn Japanese
JLPT
http://japanese.human.metro-u.ac.jp/mic-j/home-e.htmlA bunch of JLPT listening.
http://www.mlcjapanese.co.jp/Download.htmVarious JLPT resources, including listening
http://www.malago.net/jlpt.phpvarious resources for studying for the JLPT
Language Learning Blogs
http://blog.feedmejapanese.com/A blog about methods of learning Japanese. Interesting read.
http://www.alljapaneseallthetime.com/blog/The home of the (in)famous AJATT 10,000 sentence method. Many, many, many posts (but quite interesting) to go through. May absorb time.
http://www.guidetojapanese.org/blog/A blog about language learning by the Tae Kim, author of Guide to Japanese
Miscellaneous
http://www.bungeisha.co.jp/publishing/download/printable genkouyoushi that you can also type in Word with. Pretty cool.
http://www.kaomojinavi.net/index.htmcopy and paste Japanese emoticons like a pro.
http://www.myj7000.jp-biz.net/index.htm look up Kanji names
http://nihongo-e-na.com/eng/ Many, many, many links to various other useful sites
Thank you to Son for many of these resources.