A few years ago I stopped in Takayama on my way back to Tokyo from Kyoto. Lovely little historic village in the mountains (I enjoyed much more than Hakone, which felt very touristy to me). I stayed at this ryokan: http://www.honjinhiranoyakachoan.jp, which was the most luxurious in the area. The onsen, kaiseki and heavenly night's sleep remain highlights my trip. If you choose Takayama, be sure to take the walking trail around the village, which takes you through the town as well as shrines, temples and an ancient cemetery.