APA -rooms are small, some have onsen, Pay for brkfst. Lot of locations. Rates are on the higher side.
Daiwa Roynet Hotels -breakfast
Dormy Inn -breakfast & onsen
Green Rich Hotel -hotel chain in southern Honshu, breakfast, onsen, good size rooms
Hokke Club Hotels -breakfast, onsen
Route Inn – Good-sized rooms w/onsen & free breakfast
Sanco Inn -breakfast, onsen
Sotetsu Hotels – includes Fresa Inns and Sunroute Hotels
Super Hotels -breakfast, onsen
Toyoko Inn -free breakfast, cheap, sells out fast. All over Japan and international hotels. Cheap lifetime membership with good incentives
Other hotels to checkout