Nyuutou Onsen
High up in the mountains, this cluster of onsen ryokans and inns have rotenburo, konyoku (mixed gender) baths, among others, in an idyllic mountain valley setting overlooking Lake Tazawa (田沢湖).
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Noboribetsu Onsen
Hokkaido's most famous onsen and one of Japan's best, Noboribetsu's sulfur-laden waters are hot, smelly, and wonderful.
Getou Onsen
Getou Onsen is at the end of a winding, precipitous road...once you're here, you're here. Though damaged by earthquakes in 2008, Getou remains a spectacular spot to visit, and the collection of rotenburo, most of them konyoku, make for wonderful soaks.
Kusatsu Onsen
This scenic mountain onsen town is famous for its "healing" waters, steamed sweets ("manju"), and a really interesting central area called the "Hot Water Field" (湯畑) where the scalding, sulfurous water is collected and funneled off to the various inns, baths, and ryokans.
Kurokawa Onsen
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.
Kawayu Onsen
Famous for foot onsen (ashiyu, 足湯), with scaldingly hot water high in sulfur.
Ibusuki Onsen
Ibusuki's fame comes not from its waters, but from its black, volcanically heated sand. This is one of the only times where you don't bathe before entering -- simply don a yukata and plastic slippers, and walk from the changing room outside to the sunaburo (sand bath).
Hakone Onsen
Hakone is a popular onsen resort within easy reach of Tokyo by train; however, due to the vast quantities of tourists it is less friendly and less interesting than many less accessible resorts.
Echigo-Yuzawa Onsen
Seeing as the town itself is a bit over-developed and the innkeepers surprisingly unfriendly, there's not much reason to leave the train station -- with its excellent, piping hot onsen (infused with sake) and the sake-tasting salon right there, and a range of local foods/souvenirs as well, it's easy to spend an hour or two here in the station before meandering outside. Ashiyu (foot onsen) are sprinkled around the town -- be sure to sample one or two of them if you do make it out of the station.
Akiu Onsen
This quiet mountain village boasts a number of nice onsens. Though there's less traditional ambiance here, the famous gorge (pictured below) makes for a nice diversion between soaks.