Annotated Guide to Websites
Hiragana & Katakana
A good hiragana chart with pronunciation
The hiragana chart, pronunciations, and quizzes
The same for katakana as the above one
Intro to hiragana and katakana
Good site for hiragana, katakana and kanji basics
Japanese language in general
http://www.kanjistep.com/en/online/sounding/sounding.html is a pronunciation guide.

http://mysite.wanadoo-members.co.uk/nihongo/index.html Hiragana and katakana mnemonics online

http://66.110.202.42/peachstar/explorer/units/lrnactiv/hir-live/homepg.htm More hiragana and katakana mnemonics online

http://www.kanjistep.com/en/online/hiraganasteps/intro.html is the hiragana tutorial, complete with sound and practice sheets. 
http://www.nihongoweb.com/Hiraganapro/index.html is a hiragana tutorial with sound and stroke order.
We can make use of the hiragana quizzes
http://www.genki-online.com/js/hiragana1.htm
http://www.genki-online.com/js/hiragana2.htm
http://www.genki-online.com/js/hiragana3.htm
http://www.thejapanesepage.com/hiraganar.htm is a flashcard generator with excellent mnemonic tips.
Hiragana Screen Saver is just what it says it is. 
http://iteslj.org/v/jre/katakana.html is katakana reading practice.
http://web-jpn.org/kidsweb/say/katakana.html  is a good katakana chart with pronunciation. 
the katakana quizzes
http://www.genki-online.com/js/katakana1.htm
http://www.genki-online.com/js/katakana2.htm
http://www.genki-online.com/js/katakana3.htm
http://www.kanjistep.com/en/online/katakanasteps/intro.html is the katakana tutorial, complete with sound and practice sheets.
http://www.nihongoweb.com/Katakanapro/index.html is a katakana tutorial with sound and stroke order.

http://webjapanese.com/wj/game/00.html Hiragana and katakana memory game

http://genki.japantimes.co.jp/self/site/gakusyu/hiragana2.html  is a hiragana listening quiz

http://genki.japantimes.co.jp/self/site/gakusyu/sinkei.html is a matching game

http://japan.fll.purdue.edu/ultimate/ "Ultimate Kana Challenge" -- an awesome game!

http://www.csus.edu/indiv/s/sheaa/projects/hiragana.html Hiragana drag'n'drop -- this too is very cool!

http://www.csus.edu/indiv/s/sheaa/projects/katakana.html This is the katakana version.

http://www.learnjapanese.behappy.com/hiraganamap.htm  Assignment for learning hiragana by using a map of Japan.

http://www.learnjapanese.behappy.com/hiragana_assignment.htm  Part of the above assignment.

http://www.arts.monash.edu.au/subjects/japanese/sakura/lesson05/exe1.html   Hiragana recognition

http://www.arts.monash.edu.au/subjects/japanese/sakura/lesson18/exe1.html   Katakana recognition

http://www.arts.monash.edu.au/subjects/japanese/sakura/lesson01/exe1.html  Hiragana and katakana recognition.

http://www.kanatutor.com is a script for practicing hiragana and katakana recognition (thanks to Thijs Dalhuijsen!)
This is a very interesting chart that shows where hiragana and katakana come from
Kanji
http://web-jpn.org/kidsweb/say/feature/system.html is a good historical primer on Japanese writing systems.
http://web-jpn.org/kidsweb/say/quickkanji/quickkanji.html gives a very easy-to-understand introduction to how kanji evolved.
There are kanji quizzes for Japanese proficiency test levels two through four here:
http://www.asahi-net.or.jp/~tx2h-mtok/kanji/kanji4g.html (4)
http://www.asahi-net.or.jp/~tx2h-mtok/kanji/kanji3g.html (3)
http://www.asahi-net.or.jp/~tx2h-mtok/kanji/kanji2_1g.html (2)
http://gahoh.marinebat.com/modules.php?name=Content&pa=list_pages_categories&cid=5
Possibly the most comprehensive Japanese-writing site. There are hiragana and katakana charts, as well as complete indexes of kanji classified by pronunciation (indicated in roomaji), stroke number, radical, and year taught in Japanese school.
the kanji quiz (beginning level)
http://www.genki-online.com/js/Kanji_04.html

http://www.manythings.org/kanji/ has two dozen quizzes with two dozen kanjis each, quizzes on commonly-used Japanese words, a daily page with 36 kanji a day, and quizzes on words from Japanese newspapers. 
Intermediate kanji:
http://www.genki-online.com/js/Kanji_05.html
http://www.kanjiclinic.com/ This is a series of columns on kanji that appears in The Japan Times.
http://www.kanjistep.com/
The Japanese Language Resource Center has great tutorials on major subjects.
http://www.kanjistep.com/en/online/kanji100/intro.html are lessons in “the 100 essential kanji.”
http://www.kanjistep.com/en/online/weeklytest/main.html is where you find your placement: take the level 2, 3, or 4 tests (and use the stopwatch they provide).
http://www.kanjistep.com/en/online/weeklytest/placement4.html
http://www.kanjistep.com/en/online/weeklytest/placement3.html
http://www.kanjistep.com/en/online/weeklytest/placement2.html
http://www.nihongoweb.com/Courses/index.html is a list of the kanji offered in each class at the University of California at Berkeley.
http://www.kanjisite.com/
More advanced kanji:
http://www.arts.monash.edu.au/subjects/japanese/sakura/lesson21/exe1.html 
The Kanji Site is a comprehensive kanji-learning resource that groups kanji on the basis of the Japanese Language Proficiency Test level.
http://www.kanjisite.com/html/start/jlpt/index.html is where you choose the level.

http://webjapanese.com/wj/kanji-c/index.htm Kanji practice – level 4 (= 100 kanji ) and above. 100 questions. Fake log in OK. (Need to set Japanese as main default language.)

http://webjapanese.com/kanji/index.html

This site is based on Bonjinsha’s Basic Kanji Book Vol. 1 & 2. Introduces the kanji and has interactive quizzes. Readings are all in roomaji. Check for reliability. Encoding is a problem.

http://www.wfu.edu/%7Etakatay/YookosoKanji/  offers kanji for the Yookoso textbook.
Put kanji flashcards on your iPod (not free):
http://loopware.com/iflash/
Verbs
http://www.asahi-net.or.jp/~tx2h-mtok/teform.html  is a good activity for practicing the TE-form.
http://www.asahi-net.or.jp/~tx2h-mtok/naiform.html  is the NAI-form version.
http://www.asahi-net.or.jp/~tx2h-mtok/dictionaryform.html  is the dictionary form version.
http://www.asahi-net.or.jp/~tx2h-mtok/causativeform.html  is the causative form version.
http://www.asahi-net.or.jp/~tx2h-mtok/potentialform.html  is the potential form version.
http://www.asahi-net.or.jp/~tx2h-mtok/passiveform.html  is the passive form version.
http://www.asahi-net.or.jp/~tx2h-mtok/volitionalform.html  is the volitional form version.
http://www.asahi-net.or.jp/~tx2h-mtok/conditionalform.html  is the conditional form version.
http://www.genki-online.com/js/te_form.html TE-form conversion (from dictionary form)
http://www.genki-online.com/js/verb_short_forms.html changing dictionary form to negative
http://www.genki-online.com/js/verb_past_aff.htm changing dictionary form to plain past
http://www.genki-online.com/js/verb_past_neg.html changing dictionary form to past negative
http://www.genki-online.com/js/verb_potential.htm changing dictionary form to the potential 
http://www.genki-online.com/js/verb_volition.htm changing dictionary form to the volitional
Adjectives
http://www.genki-online.com/js/lesson05-1.html There are also quizzes for negating adjectives
http://www.genki-online.com/js/lesson05-2.html putting adjectives in the past tense
http://bama.ua.edu/%7Ekarizumi/language/japanese/
Adjective section looks good. Simple grammatical explanation and drills for adjectives which involve hearing the Japanese and writing the English equivalent. It ran out at level 4. Verb section not as good.
Grammar

http://homepage3.nifty.com/jgrammar/ Grammar reference site

http://myweb.tiscali.co.uk/d.mereweather/intro2.htm Some simple grammar, some simple reference material

http://www.mindspring.com/~kimall/Japanese/index.html A great guide to the grammatical principles of Japanese. The sections on particles and verbs are very informative.

Particles

http://webjapanese.com/wj/brush/index.html Particle practice – 4 level and above.

Probably good for JNL A/Foundations particle practice. Try also upper JFL2 and above.

Also has SURU or NARU, transitive and intransitive verbs,  Keigo

Daily Routine
http://www.jflalc.org/teaching/resource/comptech/cloze.doc Short cloze exercise suitable for: directions, daily routine particles.
http://www.jflalc.org/teaching/resource/comptech/Listening.doc Listening exercise for cloze exercise. Suitable for: directions, daily routine particles.
http://www.jflalc.org/teaching/resource/comptech/wrksht.doc Worksheet for My Day (level 1)
http://www.db.ics.keio.ac.jp/%7Eseto/life.html A university student’s daily schedule. ShortSome kanji.
http://www1.odn.ne.jp/taiyo/itiniti.htm Preschool student’s day. With photos
http://www.tjf.or.jp/eng/de/deindex.htm Kentaro’s Day (these are available as posters from the MS)
http://www.fujieda.ssu.ac.jp/%7Ef0021093/study.htm A school student’s schedule. Quite simple but with kanji.
Time
http://genki.japantimes.co.jp/self/site/gakusyu/clock.html is a time listening quiz
http://www.languageguide.org/txt/time/jp/ gives days of the week, months, seasons, etc.
Body parts

http://www.japanesecentral.com/Flash/body/index.html is a guide to body parts.
http://www.japanesecentral.com/Flash/body/2.html is the same.
http://www.languageguide.org/im/body/jp/ is another body art guide.
http://www.languageguide.org/im/body2/jp/ is part two of the above.
Weather
http://www.languageguide.org/im/weather/jp/ gives a good rundown of weather terms.
Numbers & Counters
http://www.languageguide.org/im/num/jp/ gives the basic numbers. 
http://www.japanesecentral.com/numbers/numbers.html is a good numbers guide.
http://genki.japantimes.co.jp/self/site/gakusyu/number.html
 is a good listening quiz
http://www.nihongoweb.com/Counter/index.html offers practice with counters.
http://web-jpn.org/kidsweb/say/numbers.html is a good numbers guide.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/counters1-memory.htm  is a good memory game for counters.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/counters2-memory.htm  is part 
Days of the Week
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/days-memory.htm  A good memory game.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/days-k-memory.htm  (Same as above, with kanji.)
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/days-order.htm  Game for putting the days of the week in order.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/days-k-order.htm  (Same as above, with kanji.)
Days of the Month
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/dates-memory.htm   A good memory game for days of the month.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/dates-order.htm   A good game for putting the dates in order.
Months
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/months-memory.htm   A good memory game for the months.
http://www.uq.net.au/%7Ezzkmunr1/jap-ex/months-order.htm   A good game for putting the months in order.
Vocabulary (including verbs)
http://www.japanesecentral.com/Flash/Clothing/index.html is a guide to clothing vocab and verbs.
http://www.japanesecentral.com/Practice/practice361.html is useful phrases in roomaji.
http://web-jpn.org/kidsweb/say/quickjapanese/quickjapanese.html offers a short list of essential Japanese phrases.
http://www.languageguide.org/nihongo/ gives a wide variety of vocabulary with accompanying audio files that give pronunciation.
Reading passages
http://www.coscom.co.jp/jungle/j-ccnews.html
News of the week.  Top news stories simplified and written in hiragana, with options for roomaji and kanji. Old stories include bird flu and revolving door accident. Vocab list with English translations included.
http://www.coscom.co.jp/jungle/j-column.html
Weekly column similar to news of the week. This week’s column is Respect for senior citizens day.
http://www.coscom.co.jp/jungle/j-column.html
Short reading materials on Japan.
http://www.coscom.co.jp/j-index.html
Links to phrase of the day, conversation of the day, kanji of the day and word of the day.
http://language.tiu.ac.jp/index_e.html
The Reading Tutor was designed to help JFL/JSL learners improve their reading skills in Japanese. This system was developed specifically to help learners study written Japanese at their own pace, in their own way. There is a “dictionary tool” that will give definitions of words within text that has been entered. There is also a “level checker” to indicate that text’s level of difficulty according to the standards of the Japanese Proficiency Test. Also available is a collection of annotated readers. 

http://webjapanese.com/column/stock01/index.html

Reading Practice for Intermediate level to advanced JFL or JNL (?gap) students. Topics include cultural and social events.

Quizzes
http://momo.jpf.go.jp/sushi/index.php?LangFlag=e
This is a very good quiz for those who have finished a year or two of middle-school Japanese.
http://a4esl.org/
A variety of quiz exercises between Japanese and English. Most of the quizzes are for intermediate and advanced students with kanji ability. These have been submitted by people who have used the quiz generator at http://a4esl.org/c/bilingual.html
The MS-friendly ones are written almost completely with kana:
http://iteslj.org/v/j/ck-countries.html  is a countries quiz (quite a few typos in Japanese, though)
http://iteslj.org/v/jre/sports.html is a sports quiz (some kanji – click on “skip” if you can’t read).
http://iteslj.org/v/j/ss-01.html
http://iteslj.org/v/j/ss-02.html
http://iteslj.org/v/j/ss-03.html
http://iteslj.org/v/j/ss-04.html
http://iteslj.org/v/j/ss-05.html
http://iteslj.org/v/j/ss-06.html
http://iteslj.org/v/j/ss-07.html  All of these offer first-year vocab
http://iteslj.org/v/j/ss-08.html
http://iteslj.org/v/j/ss-09.html
http://iteslj.org/v/j/ss-10.html
http://iteslj.org/v/j/ss-11.html
http://iteslj.org/v/j/ss-12.html
http://iteslj.org/v/j/ss-13.html
http://www.genki-online.com/js/greet_01.html the greetings quiz
http://www.genki-online.com/js/voc01_1.html basic vocab quiz
http://sp.cis.iwate-u.ac.jp/sp/lesson/j/
“Dictation Quizzes for Japanese Speech” tests your listening ability. You can choose from syllables, words, sentences, consonant pairs, long vowels, choked sounds, and word accents. There is also the ability to select by level.
Miscellaneous

http://www.mapmsg.com/games/statetris/japan/ Very cool Tetris game involving Japan's prefectures

http://www.csus.edu/indiv/s/sheaa/projects/flash/prefectures.html Geography: Identifying prefectures

http://www.csus.edu/indiv/s/sheaa/projects/flash/cities.html  Geography: Identifying cities

http://earth.endless.ne.jp/users/yoshi216/tizu-top.htm Geography: Prefecture puzzle

http://www.cjlea.org/teachers/fumikota/fumikota.htm#a1  How to use "genkouyoushi."

How to Use Genkooyooshi

http://www.trymango.com/ is Japanese lessons

http://langmedia.fivecolleges.edu/collection/lm_japan/jaIndex.html  Japanese lessons over a number of themes, with video.

http://www.hiragana-gateway.com/ Hiragana Gateway converts all kanji into hiragana. Just copy and paste in the URL of a particular site.

http://www.kfstudio.net/blog/archives/460kids/20040819083541.php Nice AIUEO chart that can be printed out and colored.

http://kids.nifty.com/study/kata_rensyu/index.htm#ai Katakana practice sheets that can be printed out.

http://kids.nifty.com/study/hira_rensyu/index.htm Hiragana practice sheets that can be printed out and colored.

http://kids.nifty.com/study/hiragana/index.htm Hiragana AIUEO poster that can be printed out.

http://kids.nifty.com/study/katakana/index.htm Katakana AIUEO poster that can be printed out.

http://inmotion.magnumphotos.com/special/tokyolovehello.aspx Great photo/audio collage of Tokyo.

http://big1file.googlepages.com/jdico Extensive Japanese dictionary index (in Japanese) index

For Anime & Manga fans
http://dora-world.com/
Doraemon Channel
http://jump.shueisha.co.jp/home.html
Shonen Jump
http://www.shonenjump.com/
Shonen Jump (US)
http://www.tv-asahi.co.jp/shinchan/
クレヨンしんちゃん
http://www.nhk-sw.co.jp/chara/sakura/
Card Captor Sakura
http://www.cartoonnetwork.co.jp/toondata/
Cartoon Network
For teachers: Professional Development 
http://clear.msu.edu/about.html
One of the main organizations devoted to computer assisted language learning (CALL) in the USA. 
http://llt.msu.edu/  is a link to an excellent journal.
http://www.cortland.edu/flteach/flteach-FAQ.html
FL Teach is the premier listserv for foreign language teachers. This is a collection of the many questions and answers that have been exchanged over the years. It is a goldmine of information on foreign-language instruction.
For teachers:  Resource Development
http://clear.msu.edu/teaching/matic/index.html is the “Game-o-Matic,” a generator of eight different types of computer activities. (Some of these are not Japanese compatible.) 
http://www.iwai-h.ed.jp/~irie/javascript/webquiz/ A materials generator.
http://www.jflalc.org/teaching/resource/comptech/YesNo.doc Yes/No card template. (Happy & sad face)
http://japanesecentral.com/Siryoo/pictureclips/index.html Downloadable visual aids: useful for making flashcards: clothes, music sports, music, professions, etc.
http://web.uvic.ca/hcmc/clipart/ Language teaching clipart library
Sites with multiple resources. Some need further exploration 
http://www.japanese-online.com/NonMem_JLL.htm Japanese-Online.com has its own 16-part basic Japanese series with an audio component. It is very compact but practical.
http://www1.linkclub.or.jp/~yokozawa/nihongo4u/index.shtml Japan Teaching Material Library has a wealth of materials available.
http://momiji.jpf.go.jp/kyozai/index.php “Minna no kyouzai” site: many many materials for teaching Japanese.

http://www.manythings.org/japanese/links/ A site to be explored

http://www.ccet.ua.edu/nihongoweb/ University of Alabama Nihongo Web

http://home.earthlink.net/~royk4/NIHONGO.html  A collection of other sites – needs exploration

http://www.asahi-net.or.jp/~tx2h-mtok/jalearn_j.html “Tokyo Tokyo Tokyo” is a big, complex cultural grab-bag. There are some good language-related activities.
http://www.genki-online.com/ This is the Genki package, which is an integrated course in Japanese. 
http://www.nihongoweb.com/ Nihongoweb is a huge resource.
http://www.usc.edu/dept/LAS/ealc/jlp/fun/fun.html Japanese for fun combines cultural notes with language and a bit of humor.
http://web-jpn.org/kidsweb/say.html is a kid-friendly guide to the basics – as well as a good “dummy’s guide” for adults.
http://polyglot.lss.wisc.edu/lss/staff/erica/CALL/
http://webjapanese.com/

http://www.lavasoft.com/ Look further

Culture
http://web-jpn.org/kidsweb/index.html A cornucopia of resources on cultural matters pertaining to Japan.
Miscellaneous

http://www.epochrypha.com/japanese/methodology.html

Some reflections on self-study

http://www.mindspring.com/~nihongo/

Nihongo Learning systems, Kana, Kanji and Gairaigo drills for Windows – software for purchase.

http://lc.byuh.edu/swallt/index.html Thanksgiving conference

http://www.nobi.or.jp/i/kotoba/hayakuchi/ A collection of tongue twisters. Long and not easy, but might make for a good “ice-breaker” at the beginning of class.
http://japanlore.googlepages.com/origami Origami sites of all kinds

The original list (some have been explored, some have not).

http://www.kokken.go.jp/index.html

http://www.ajalt.org/

http://www.jpf.go.jp/j/index.html

http://www.bonjinsha.com/

http://nihongo.kokken.go.jp:8080/jsp/index.jsp

http://clear.msu.edu/about.html

http://a4esl.org/

http://web-jpn.org/kidsweb/index.html

http://www.carla.umn.edu/

http://aci-hayama.soken.ac.jp/

http://www.tjf.or.jp/deai/

http://www.mc.maricopa.edu/~emiahn/

http://www.cortland.edu/flteach/flteach-FAQ.html

http://www.menet.ed.jp/edu/gahoh/gahoh/homej.html

http://home.att.net/~robertayoung/jessi/index.html

http://nihongo.kokken.go.jp:8080/jsp/index.jsp

http://www.jflalc.org/teaching/index.html

http://momiji.jpf.go.jp/kyozai/index.php

http://www.nobi.or.jp/i/kotoba/hayakuchi/

http://202.245.103.49/kenshu/default.html

http://www.sussex.ac.uk/languages/1-6-6-6.html

http://polyglot.lss.wisc.edu/lss/staff/erica/CALL/

http://www.sussex.ac.uk/languages/1-6-6-6.html found much of this on Monash U site.