Dean Fujii: Best kept onsen secret within Tokyo metropolitan area. Seven kinds of natural, outdoor baths (rotemburo) - fantastic on chilly winter days. The two-hour plan is reasonable, pricey otherwise.
Mana A: Not only is there an onsen, there is a shared area for men and women with massage jets, sauna, and outdoor/indoor hot tubs so don't forget your bathing suit! (Or you can rent one for ¥450)