Ryokan Warabino is a charming ryokan set in a little mountain town in Nagano. We stayed two nights, and to our surprise, they changed the menu the second day for us. The food is fantastic, healthy fare. If you're planning on staying just at the ryokan and not leaving during the day, make sure to bring lunch, as there's no other food around except for oyaki (steamed buns filled with vegetables, fruit, etc) at a place next door. There are three onsens on the property. Two are free: a rock bath and a wood bath with outside view, with each assigned to men or women for half the day and then switching. There's a private onsen outside that you can rent for 40 minutes for an additional fee. Water is clean in all of them. There's also a public onsen right next door, which you'll get tickets to when you check into Warabino. Highly recommend checking out the public onsen as well, as it has nice outdoor views. Make sure to bring your room towel and soap/shampoo from the lobby when you go to the public onsen. The ryokan is a bit difficult to get to, but they have pickup and drop-off service from the nearest station, Suzaka. It snowed the whole time we were there, so we didn't do much exploring of the local towns, but it was lovely nonetheless.
Note: There is no private shower in the room, even the rooms which do have a bathroom. You need to use the showers attached to the onsens regardless of the room you choose.