Lexilogos Online Japanese Keyboard Very useful for when you don't have a Japanese keyboard installed on your device. Handles Hiragana, Katakana, and Kanji.
Hiragana Stroke Order There are lots of stroke order diagrams available online. This is my favorite for Hiragana.
Kanji Stroke order Again, there are lots of sites that show Kanji stroke order, but this is my favorite. The only drawback is that you have to enter the actual Kanji, you can't search based on Romaji. Use the Lexilogos keyboard above, if needed.
Japanese verb conjugator This is a remarkably handy (ultra handy?) verb conjugator for Japanese. Even after learning all the conjugation rules, there are times that something like this comes in handy.
Jim Breen's WWWJDIC Jim Breen (a linguist from Australia) has a nice web site with dictionaries, a translation service, Kanji lookup, etc. There's a lot of useful information available here.
Meguro Language Center The Meguro Language Center in Tokyo has been around for quite a while and provides a wide variety of free resources for learning Japanese. Worksheets, language self-assessment, sample JLPT exams, all for free (as well as paid lessons in Japanese). MLC uses Japanese For Busy People as the basis for their language school, which is an excellent course designed by AJALT (Association for Japanese-Language Teaching).
CosCom CosCom Language Service fills some important gaps in learning the Japanese language. This is one of my favorite sites because it offers short news articles with translations and an extensive explanation of the vocabulary and grammar. Until the Slow News In people add Japanese, this is the best you can get. You get a lot of exposure to common words and phrases that you don't get until much later in a traditional language course. In addition, you can get a lifetime subscription to all of their services for around $65.00. That's cheaper than a traditional set of language learning books. Highly recommended.