Hi Victoria, The best one I've stayed so far is Guest House Rojiura in Beppu. I wrote about it on Japan Travel and listed all the reasons why I liked it. The photos I took also show how nice, clean, and convenient the place was. http://en.japantravel.com/oita/guest-house-rojiura/32955
Most of the guesthouse/hostel I went to were good (or really good). Here are those that I remember beeing nice, with some comments for the best one. I stayed of one night only in many of them. It was back in 2011-2012.
As from my experience, all of those listed are relatively easy to access from the train, or a tram (or at least at a walking distance), all were cheaper than the cheapest hotel, and no complain about how clean it was.
Guest House Pongyi - Kanazawa
When I arrived, I was invited to participate to their okonomiyaki party, that would be a couple of hundred yen. It felt really welcoming and was a nice introduction to cooking okonomiyaki.
Hana Hostel - Kyoto/Hiroshima
J Hoppers - Takayama/Osaka/Hiroshima
I appreciated all the hostel from the J Hoppers/Hana group, and they had a fidelity card that you can stamp at each stop to get a discount or gift after a numbre of nights.
Sen Guest House - Matsumoto
Yuzan Guest House - Nara
Guest House Fujihotel - Onomichi
Hostel Akari - Nagasaki
Nakashimaya - Kumamoto
K's House Mt.Fuji - Fujiyoshida
In this list, I did not include the one that I did not like as much, but they were not horrible, maybe they just did not feld as friendly, or one that did not had personal locker (nobody stole my things, but you do not feel as safe).
Ishiba Ryokan in Hiroaski was great! Cheap, friendly, atmospheric, and close to the sights.
For hostels, I stayed at a great one in Dogo, and recently K's House Kyoto. There's also a K's House in Ito which is lovely, an onsen turned into a hostel