I thought Hakone was lovely, very traditional onsens (hot springs) if your into that kind of thing.
If you can get across to the Fujimi Panarama bike park its worth a crack, the hire bikes there are not too bad.
Yoyogi park in Tokyo is always worth a walk around on a Sunday for taking in the locals dressed up.
Japan is an amazing country, been to a few places around Tokyo, Osaka, Kyoto and on Okinawa but generally its all good and for getting around the train system is excellent.