I have learned the most of what I know of Japanese in the web.
Web cannot be the only resource, I also have a lot of friends to ask to...
But I'd like to tell you the resources I found on the net. I used some for a long while, some only for a bit, but I think all of them are worth a deep glance.
Everyone should find the sites that work better for him/her.
This is my selection.

Written lessons

They are quite useful to start to get familiar to the language. You can learn something about the basic grammar and some basic vocabulary at the same time.
http://www.learn-japanese.info/indexg.html
http://japanese.about.com/library/mmore.htm

Hiragana and katakana

Do you think you can get fluent with Japanese only using romaji? Maybe you can, but you wouldn't have the pleasure to read! The two alphabets are not so difficult... and remember that all foreign words are written in katakana... it means you could probably understand them if you are able to read this alphabet!
http://smart.fm/series/3322
http://japanese.about.com/library/blhira.htm
http://japanese.about.com/od/howtowritekatakana/How_to_Write_Katakana.htm
http://www.youtube.com/watch?v=vZDukruw4ac

Audio lessons

You cannot communicate or watch dramas and animes if you don't know how the Japanese language sounds like. I found some courses, some are a bit difficult for true beginners, or the most of the material is not for free. You need to check what's on there often.
http://www.nhk.or.jp/lesson/english
http://www.japanesepod101.com/
http://coelang.tufs.ac.jp/modules/ja/dmod/

Video lessons

They are useful to connect what you read and what you listen, a good way to review. I found a very basic course and another one, maybe not too simple but quite funny.
http://www.youtube.com/user/Aploosh
http://nihongo-dekimasu.blogspot.com/search/label/Nihongo%20Dekimasu

Online dictionaries

A real dictionary made of paper will help you more than any resource online (refer to this article by Brett) but actually they are useful! Sometimes is difficult to find the right Japanese word when you give the English translations... there are too many results. Try to check the results within sentences.
The data bank for the following sites is the same, only the interface is different. The second is nicer, but when you have different kanjis for the same word, the first one woks a bit better.
http://www.csse.monash.edu.au/
http://jisho.org/

Tandem

One of the best ways to learn a language is to communicate. These are good sites to know Japanese natives who are looking exactly for someone who speaks your language!
http://lang-8.com
http://www.livemocha.com/
http://www.myhappyplanet.com/
http://www.palabea.net/

Grammar

It's good to learn vocabulary and to attend to some courses, but sometimes you need to focus on grammar and grammar only. I give you the link to the most important site and to a couple of sites I found useful.
http://www.guidetojapanese.org/
http://www.gwu.edu/~eall/vjg/vjghomepage/vjghome.htm
http://thejapanesepage.com/grammar.htm

Flashcards

When you need to relax a bit, when you want to learn vocabulary and some sentences, flashcards are the answer. Things stick to your mind and you even don't realise it! Try not to get addicted.
http://smart.fm
http://www.livemocha.com/
http://www.readthekanji.com

Kanji stroke order

OK, you can now read everything. But to write kanjis is a bit different. You must learn the stroke order, otherwise nobody will understand what you wrote. And sometimes the font is not exactly the same as when you write down the character.
http://japanese.about.com/od/kan2/Kanji.htm
http://www.yamasa.cc/members/ocjs/kanjidic.nsf/SearchKanji3?OpenForm
http://www.jlpt-kanji.com/

Write a journal in Japanese

It's a good way to show to the world that you can indeed say something in Japanese. No matter if you make mistakes, you can explain what you mean in English. And probably someone will correct you or reply to your message... in Japanese!
http://smart.fm
http://lang-8.com

Attend interactive lessons

Even if not in the real world, they can be valuable, and you can stay at your beloved desk! But since you are here, you probably know what I am talking about!
http://edufire.com/search/courses?q=japanese

Chat

So far I found only a good chat where you can chat with English speaking people about Japanese. It can be indeed useful, there are always people willing to help!
http://www.studyjapanese.org/

Watch TV

Here you can find some anime and drama with English subtitles! Get used to the words, and try to write down some new words you think you understood, in order to listen actively and not passively!
http://asianrice.tv/browse/Japanese
http://www.veoh.com

Be curious and never lose motivation! *NEW*

What I mean is... Try to look for something that suites you. Sometimes you stomp on useful material on YouTube or Google, while you were trying to find something completely different. Instead of looking for "study Japanese", go for "日本語勉強”. Use ”日本語会話” instead of "Japanese conversation". Maybe you will find something useful for a friend who is studying Japanese and not for you... Don't get mad! Help your friend, and you will be helped in return! You will feel better because you helped someone, and you will be able to share an experience, one of the best ways to keep the motivation at the maximum!
This is one of the reasons why, from time to time, in this article I add resources, when I find something useful!

In the most of the listed sites there are many other things to do... Exercises, reviews, contents about Japanese culture! I cannot list everything here, and I want you to discover your own way to enjoy some of these sites!