On this page I shall list different websites that I have found useful over the years in my learning, from beginner right up to university! I can't put everything up because theres so many! But if anyone wants me to recommend a website for something, even if its only for fun learning, I will be more than happy to oblige!
http://www.realkana.com/ Very useful for learning hiragana and katakana. Its essentially a kana flashcard website, but you can change the fonts etc.
http://www.kantango.com/ Another flashcard website but for kanji and vocabluary. On here you can create your own account and make your own word lists. You can also use word lists from other peoples accounts, which can also be useful as you can often find people with things like the JLPT vocab lists up.
http://japanese.about.com/ A wide variety of information on here, including small exercises and phrases you can do daily. They also have a email subscription so you can get articles emailed to you as well! They author of the page keeps articles seasonal which is nice. Would be useful for beginners and veterans alike!
http://nihongo-e-na.com/eng/ Generally good for finding learning resources.
This http://language.tiu.ac.jp/index_e.html ,this http://www.popjisyo.com/WebHint/Portal_e.aspx and this http://www.rikai.com/perl/Home.pl are useful reading aids. You copy and paste what your trying to read into the programme, and it will give hints and dictionary explanations when you hover your mouse over the words that your stuck on!
More fun things to do (but still mildly useful)
http://www.ehonnavi.net/ This website carries tonnes of Japanese Childrens picture books（絵本）that you can read online if you set up a free account. The only downside is you can only read each one once for free.
http://anime-manga.jp/ This site is rather fun, but all the vocabulary is based around different manga genres. Its not necessarily useful to learn how to speak like an Edo Period Samurai! The school and romance ones maybe. Its got a good format and is aimed at different levels, but I would only use it as a supplement for learning.