This is not a study guide, and it may not be an effective route to learning Japanese. It's a roundup of my Japanese learning activities, created primarily as self-documentation and secondarily as a source from which others may pick what seems useful to them. I'm by no means fluent in Japanese. To claim so would be an insult to anyone more dedicated to learning and more proficient in the language.
Last update: February 2013
I started learning Japanese about three years ago, not as a student in an official institution, but on my own accord and in my own pace, while finishing my degree and later working full-time. After these three years, I am able to read manga and easy novels quite smoothly with the aid of a dictionary. I can hold reasonably coherent everyday conversations, but am not yet fluent, nor generally confident of being understood and understanding. I was able to find my way around Japan as a tourist speaking mainly Japanese, though. I can understand the gist of everyday speech, e.g. watch most anime without English subtitles. Recently I was certified with JLPT N3. See the official test page for the language skills expected at this level.
What I've learned from this is, in short: Japanese is hard, but it's possible to make continuous significant progress even when learning it as a hobby. It requires more effort than most languages, especially for speakers of European languages. But from my experience, there's a sense of advancement and practical reward at any stage.
Learn kana and kanji starting from day zero. Avoid textbooks which don't deal with kanji or even kana. You'll have to deal with real written Japanese some day anyway. Or else, be stuck on a grade school language level forever.
Use the Heisig method for learning kanji. Kanji are ideograms, associated with a mental concept. Sounds are a secondary concept. This is why the Heisig method (as described in Remembering the Kanji Vol. 1, ISBN 978-0-8248-3592-7, here is a free sample) worked for me: associate an English keyword with the writing of the character by means of an mnemonic, and memorize this by spaced repetition. Use spaced repetition tools like Anki or the website Reviewing the Kanji. You can do this independently from any knowledge of Japanese vocabulary and grammar, so this is the first thing I did.
Actually write down the kanji when learning, with a pen. It's quite hard to remember a mental picture of a kanji. It's easier to remember a sequence of hand movements (the strokes you do with your pen). The sheer number of kanji to be learned (more than 2000) can be broken down into a much smaller combination of discrete stroke patterns, called primitives by Heisig (less than 100).
Don't worry about "forgetting" unused kanji. The English keyword is only of temporary use and will eventually fall away when you acquire actual Japanese vocabulary. I finished the book front to back, in the course learning 2000 kanji with 2000 English keywords. At some time in the intermediate between finishing the book and now, I forgot how to write most of these kanji. I learned not to worry about that, because they will come back in the next step, when they are actually needed and used.
Start memorizing all kanji again, this time with Japanese cues. Create an SRS deck yourself, using vocabulary that you actually know and use regularly. For the cue, use one or several words with the kanji crossed out and added furigana. When several readings exist, try to include them all. By this, you can add the reading(s) to your already existing mnemonics between writing and meaning. Add the kanji ordered by frequency (see here for the ordering that I used), rather than the Heisig order. In the course of re-reviewing the kanji, you will also recall from your memory the writing of the kanji that you forgot since learning them with English keywords - turns out, you never really forgot them.