These are web resources that you might find useful in studying Japanese. Big thanks to Rico who wrote the following guide.

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Rikai

http://www.rikai.com

Rikai is one of the most useful tools for learning Kanji. Using Rikai, you are presented with a pop-up window that presents information on Kanji that appear on a webpage. Information is given on the word as a whole and for each individual Kanji. The definitions are taken from Jim Breen's WWWJDIC dictionary.

When using Rikai.com for the first time (or if you ever clear your cookies), be sure to click on the drop box on the upper right and select "Japanese to English."
Rikai presently comes in two flavors:

Web Site:
The Rikai web page gives you two options. You can either type in URL or paste a block of text and Rikai will process the data immediately.
Rikai XUL Plug-in:
This plug-in only works with Firefox. With the Rikai XUL, you no longer have to visit the Rikai webpage. When visiting a page, you simply choose "rikaixul." Processing will take place in the same matter as on Rikai.com.

Pop Jisyo

http://www.popjisyo.com

Basically, the same thing as Rikai. You might like this better. This site can also process Spanish and Korean.

WWWJDIC

http://www.csse.monash.edu.au/~jwb/wwwjdic.htm

For those who don't know, this is the web's premier Japanese-English dictionary. In fact, many web tools (for ex Rikai) make use of Jim's EDICT dictionary. You can search for Japanese words, either in Japanese, Romaji, or English.

Flashcard Exchange

http://www.flashcardexchange.com
This site is perhaps the largest flashcard study site on the web. There are over a million flashcard sets available (covering many topics, not just Japanese). Luckily for us, Kanji seems to be a fairly popular topic. Of particular interest is that there are flashcard sets for James Heisig's Remembering the Kanji Vol.1 book. Of course, There are many other Kanji sets as well. This is the perfect site for creating web flashcards and quizzing yourself. You can quiz yourself either in the order that your set was created or at random. For the studious, I would suggest making flashcard sets for articles that you read and just periodically come back to the site and quiz yourself.
 

JLPT-Kanji

http://www.jlpt-kanji.com
For those studying for the JLPT exam, this is the best site for studying. Similar to Flashcard Exchange, you can create flashcards. However, the real power of this site comes in the fact that it is organized by JLPT level. It takes the Kanji required for every level and organizes them into sets of 30 Kanji. You can study these sets in either normal or random order.

Tensei Jingo

http://www.asahi.com/paper/column.html
Another common way to build vocabulary is by reading newspaper articles. One of the most famous newspaper columns used by Japanese learners is "Tensei Jingo." Essentially, this is a public opinion article that discusses views on current events affecting Japan. Since it's an opinionated column, the language is somewhat more liberal than the conservative, dull manner in which most articles are written.
One major benefit is that there is a new article every weekday. From Monday to Friday, you can wake up in the morning and have a new article to read. This is great for Japanese learners that prefer to set aside a chunk of time everyday for studying. Lastly, the size of the article is usually only three or four small paragraphs. So it's very manageable read.
 

Nuthatch

http://www.nuthatch.com/kanji/demo/radicals.html
This link here is a rare find. It is a listing of Kanji organized by radical. When you click on a Kanji, you're presented with all sorts of useful information. An interesting use of this site is for attempting to decipher handwritten Kanji. As you may soon figure out (unless you're from Kanji-reading country), deciphering handwritten characters is nearly impossible. For those special cases, a good strategy is to try to figure out what the radical is and look through this index. In most cases, you'll find that only one or two Kanji look similar to what was written down.

Another cool feature is that this site has a "Kanji Jump" feature. When looking at Kanji compounds, you can click on any individual Kanji and study that character.  

Pera Pera Penguin

http://www.yomiuri.co.jp/ppp-e/
Without a doubt, this is perhaps the best grammar review on the web. "Pera Pera Penguin" appears once every 5 weeks in the Daily Yomiuri, one of the most popular Japanese newspapers.
Foreigners from all over Japan mail their questions to the author and one letter is chosen to be the topic for a column. Often, these articles focus on topics that have confused Japanese language learners for quite some time. It's great for learning material that you would never encounter in a textbook or course.
Even on simple topics, you will always learn subtleties that you never even knew about. Finally, the author adds a small column for vocabulary to ensure that you will learn new words every week. Usually these words are related to the article topic.  

Kanji Clinic

http://www.kanjiclinic.com
If you've ever been frustrated with Kanji, this is the site for you. Kanji Clinic is the de facto website for researching approaches to studying Kanji. Through articles and book reviews, Kanji Clinic critically evaluates various Kanji-learning methods.