I think japanesepod101.com is a great one. I also recently discovered smart.fm, which has motivated me to study more than anything else I've ever tried.
Lang-8 is great for writing, and native speakers will correct your Japanese (and you can in turn correct others English, or whatever other language you are native/fluent in). It's free, as it's community-based.
Other than that, there's great apps for the iPhone/iTouch. iKanji is excellent for learning meanings, readings, and stroke order (you can even practice the stroke order!).
Those are what I use the most and find the most effective thus far. I've also found a site, though I don't remember the name just now, that allows you to take classes or teach classes to others trying to learn your language. Some are free to take, for conversation, others cost maybe $10-75 (American dollars) depending on how good the teacher is, what they do, etc. I haven't tried it yet but it looks like it could be helpful.