Does temple experience at Koyasan in Wakayama count? Same as ryokan, just that you have to wake up early in the morning to attend their prayers.
Went to the tourist information, asked for the cheapest temple available, and they helped book a 9500yen stay. That was 21st Dec, before the peak traveling period.
Live life in Sepia at Kaneyoshi Ryokan in Osaka. The prices used to be like the 1960's, in keeping with its retro decor. But its prime waterfront position and its discovery by the masses (I am guilty as charged) means that it is gone up from 7000 yen in the past to 13,000 yen now. Book during the off peak period for extra value. http://en.japantravel.com/osaka/kameyoshi-ryokan-osaka/4130
You can also book this on JapanTravel's own hotel site. http://hotels1.japantravel.com/templates/382834/hotels/343311/overview?lang=en