Kotohira Onsen is a simple, family style day bath tucked next to a river. A variety of rooms offer different baths, ranging in price from about 2000 yen to 3500 for 60 minutes. As with most kazokuburos, the water is poured fresh each time, allowing you to add cold water if necessary until it's just at the temp you like. Separate male and female baths are also available, and some nice rotenburo.
Edoyu is a great spot for people looking for an onsen experience without leaving Tokyo. Though on the pricey side, Edoyu offers a variety of baths and a variety of other services (massage, etc). Most unusual, it is open all night -- offering those willing to forgo a hotel a very reasonable overnight option.