Here are some tools and sites I've used in my study.
- jisho: online dictionary based on JMDict and other sources. For kanji, a convenient "Radical" lookup helps you narrow down kanji matches by choosing multiple parts (and not just its radical).
- Japanese (iOS app): offline dictionary and flashcard/SRS app for iPhone. The app name is generic enough that it's a bit clumsy to explain to others ("yes, but what's the name of the app?"). I'm currently on the N4 group of 4,000 vocabulary words (learned or memorized about 1600).
- NHK Easy News: short news stories of current events, with furigana and footnotes. I have a web tool to help extract text (with furigana) for printing; see my GitHub page.
- Ruby HTML code generator for furigana: my own tool to help you write furigana in HTML.