I have been to Japan by myself many times. Spent my late teens to early 20's there on a working holiday.
Depends where you're going, where you want to stay and whether you want to associate with gaijin or nihonjin while you're there.
If you want gaijin company, stay at youth hostels and join tour groups. If you want nihonjin company, stay in ryokan, or japanese style accommodation and talk to the people there. Often the proprietor is very helpful.
Before I became a travel agent, I spent most of my travel accommodation in Japanese inns from the Japanese Inn Group.
JAPANESE INN GROUP
Some of them are dodgy, but they're cheap and easy to book. Have a sensational time and let us know how your stay went when you get back!
HTH!