Guest House is getting famous herein Japan. You can find it almost in most of big cities. Most popular places would be Tokyo, Kyoto and Okinawa. Especially in Okinawa, it is very common to stay at guest house. There are hundred guest houses which can be searched in Internet. Below is one of the major search engine for Japanese Guest House. Try to find interesting guest houses,
http://www.guesthouse-engine.com/english.html
If your PC can read Japanese letters, it would be much fan to use the word "ゲストハウス" to search guest house. The meaning of that word is "guest house".
One thing you need to be careful is there are two meanings in the word "Japanese guest house". One is, as you suppose, hostel or hotel like. Another is kind of residence. It seems much Japanese are trying to use resident type guest house thinking it's price as well as Foreigners are doing. If you are interesting in share house, this type of guest house will be very exciting. Below site offers you share house in some area. You can also try to find share houses by using Japanese word "シェアハウス" (Meaning: Share House).