Recently has risen to top slot status: Kurokawa is a quaint, riverside onsen town with numerous onsen ryokan and minshuku all clustered together. It's a nice spot to spend a weekend -- most people simply walk from bath to bath, and the town offers a 3-bath pass which gives bathers a discount if they choose their spots carefully.
Getting to Kurokawa Onsen is tricky -- it's best to come by car; otherwise, you'll need to rely on infrequent bus service as there are no trains. Still, once you're here you'll find yourself with dozens of wonderful baths to choose from, a huge variety of places to stay, and some nice restaurants. All tucked into a quaint little stretch of riverside.