Arima onsen - very small town on the opposite side of a mountain by Kobe
-I am planning a weekend getaway there soon. I won't be staying in town as the hotels are very expensive. However, the onsen waters with their healing properties are spectacular from what my coworkers have told me. It is about a 1 hr trip by local trains/bus from Kobe.

Gero Onsen - I have been here. Lovely small town in Gifu Pref. with two outdoor public baths and many hotels with onsen built in. I would recommend this place for maybe a 1-2 night stay. Not much to do in town (literally), though you can enjoy Hida beef (which is quite famous and quite delicious!)

Kyushu - has a TON of onsen that are both famous and somewhat off the grid for tourists. If you have the time, then look into them.

edit- re-read your post, perhaps Nagano ken would be more preferable for you? Lot's of onsen there, and if you have the time you may even pop by Matsumoto castle!