There is no one best way to learn Japanese, except to be in a conversation program and live in Japan among the Japanese. Living with many others who speak your native language will not be helpful.
Here is my feeling about some of the programs for studying conversational Japanese:
1. Rosetta Stone. I borrowed someone's intermediate program. For learning vocabulary and listening to speech it is very good. For learning kanji and kana it is helpful. For speaking and listening it is not too good. People you meet, even when using polite Japanese just do not speak the way used in this program. Maybe the beginners program would be good, but I did not try that as it is too easy for me. I returned the intermediate program which I would have been willing to buy if it had been more realistic. Rosetta Stone uses strange ways to say things, which can be easier to say and usually shorter in sentence structure. Japanese syntax is hard enough without using the suggested ways used in Rosetta Stone. They are not exactly wrong in how they translate and, maybe, if you learn Kanji it is the way a newspaper or journal would state it; but not for conversation.
2. Japanese101.com. I have used this when I was really into learning this language. I joined their trial program and downloaded the lessons to my iPod. If you played the lessons over and over again I think you can learn a lot. You have your choice of 'newbie' to 'expert', so there is something for everyone. By paying for the subscription you have many ways to help you in your studies and if you apply what you learn in your everyday life, speaking Japanese, I think this program is excellent. Remember I am mainly interested in conversational Japanese.
3. School and university courses. Most of the courses given are not specifically for conversation, but they do force you to learn vocabulary and sentence structure. Using an immersion course in Japan really helps, but once again, if the course does not spend most of the time teaching conversational Japanese, your speaking on the street will be limited. If you primary goal is to learn vocabulary, Kanji and stentence structure, this is a good way to do it.
4. Miscellaneous programs. Tapes, CDs, internet programs all have a place. I have one CD program that is good by Pimsleur (intermediate), which I use to listen to going to and from work. It is pretty good and I would recommend it. I cannot say it is better than Rosetta Stone, but it is more natural for conversation, in my opinion. Another program called Power Japanese is good. You listen and answer quizzes, try to follow directions, etc. It is challenging and rewarding, but I believe it is mainly for the intermediate student. Trying to find partners on the internet is difficult if you live in the U.S. and want a partner in Japan, due to the time difference.
I am sure I have left out other ways I have tried, but the point is that no matter which method you use to study, you need to speak everyday with native Japanese.