Compared to languages like English or Spanish that use the familiar latin alphabet, for learning Japanese many more software tools end up being useful. I've been studying Japanese for several years now, here are the three sites that I use every day.
Given that no handwriting recognition software in English seems to work properly yet, I was surprised to learn that it actually works really well in Japanese. On this site you can sketch a Japanese character with your mouse and the site recognizes it and provides links to wwwjdic to see the meaning. It even guesses what you are probably trying to draw even before you finish drawing.
The algorithm is based on the order and direction of the strokes that are used to draw each character, so you need to know the correct drawing order. 90% of the time I find the character I am looking for right away, but sometimes I need multiple drawing attempts, usually because of a subtle mistake I am making in the drawing order.
As you might expect, a dictionary comes in handy when learning a language. Wwwjdic has been around for a long time and is epic in its scale, containing not only common translations but also example sentences, technical dictionaries and almost any information you could think of about the Japanese characters themselves.
Hover your mouse over Japanese text to reveal the meanings of kanji and kanji compounds. You can paste in text or website links. Extremely useful when I need to quickly read Japanese language websites without having the time to really learn all the new kanji on the page. Not only that, but I find myself using it even as a dictionary; when I encounter kanji compounds that I know how to read but don't know the meaning of, Rikai gives me a translation a bit more snappily than wwwjdic.
If it seems I'm missing some useful sites, you can contact firstname.lastname@example.org to suggest an addition.