I have stayed for months at a time specifically at Manboo NetRoom’s for about $160 a week. Highly recommended. I believe they only have locations in Tokyo though. In Osaka and Kyoto I would recommend Media Cafe Popeye’s.

I have full video tours of Manga Cafe’s as well as Net Room’s like these on my channel, Ken Loves Japan. I’ve stayed at these places for months at a time. They’re great deals. If you are in Japan and you are staying instead at hotels or hostels, you’re just throwing your yen away.