Couple things: are you Asian? If not, please limit your stay to 2 weeks like a good foreign tourist should.Originally Posted by sangai
Most major carriers fly into Japan, especially Asian airlines. Tickets used to be pretty cheap ($1000 from the States or the middle east), but with fuel prices on the rise, it's getting up around $1300.
I don't think there are any places cheaper than youth hostels that charge around $30. Capsule hotels charge around $40, but I wouldn't recommend them. No privacy, no peace and quiet, no security for your belongings (unless you use coin lockers), and it's pretty cramped and seedy. You can get a decent hotel room for $60 depending on where and when you travel.
One trip I went from Osaka to Fukuoka then up to Sapporo and back to Osaka in 3 weeks with plenty of stops in between. It's fun if you enjoy train trips, which I do. It's also a good way to see the difference in culture and people between the regions of Japan.