Kusatsu in Gunma, Hakone in Kanagawa, Kinugawa in Tochigi, Tokachi in Hokkaido, Dogo in Ehime, and Beppu in Oita are among my favorites. But Ogori has a civic onsen and is only ￥270 for city residents after 6:00PM!
The Yufuin-no-Mori limited express train from Hakata to Yufuin in Kyushu is very nice, too. I took it for the first time two years ago with my wife. We'd been wanting to ride the green train since it was one of our son's favorite when he was a train-freak toddler. The train slows down and lights are dimmed to see the waterfall that is clearly visible as the train passes alongside the Chikugo River. That trip was memorable!
Kusatsu in Gunma, Hakone in Kanagawa, Kinugawa in Tochigi, Tokachi in Hokkaido, Dogo in Ehime, and Beppu in Oita are among my favorites. But Ogori has a civic onsen and is only ￥270 for city residents after 6:00PM!