Shortlisted a few at the moment. Pls contribute if you know of any nice place to stay especially for Kyoto. Preferably < 4000 yen per night.
Osaka:
http://www.yougendo.com/about/index.html
http://www.asiarooms.com/japan/osaka/sunlife.html
Kyoto:
http://www.kyoto-ap.ne.jp/sanki/index-e.html
Osaka:
http://www.yougendo.com/about/index.html
http://www.asiarooms.com/japan/osaka/sunlife.html
Kyoto:
http://www.kyoto-ap.ne.jp/sanki/index-e.html