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.
Considering how near it is to Tokyo, Hakone is quite expensive to visit -- requiring a private train line, taxi, or infrequent local service. The baths here tend to be somewhat lukewarm and many are spa types within massive hotels rather than quaint, quiet spots to soak and relax. If you've only got a few days in Tokyo, you're better off visiting some of the closer day-trip baths, but if you want to escape the city and don't mind a lot of company, then Hakone may suffice. Nearby Atami is easier to get to and has the advantage of being near the seashore. A well-planned weekend can take in both of these resorts.