By plane
The nearest airports to Hakone are in Tokyo. Note that if you have a reservation at a ryokan in Hakone, unless your plane lands in the morning, it is recommended that you spend your first evening in Tokyo or Yokohama, or else you might miss out on (and be charged for) dinner at the ryokan, or worse, you may be locked out of (and be charged for) your room at the ryokan's curfew time, if there is one.
Allow about 2 1/2 to 3 hours to reach Hakone from Narita Airport by train, and about 1 1/2 to 2 hours from Haneda Airport.
By train
The fastest and most expensive method of reaching Hakone from Tokyo is to take a Tokaido Shinkansen Kodama train from Tokyo to Odawara, then transfer to the Hakone-Tozan Line for the run to Hakone-Yumoto (trains operated by Odakyu Railway). The one-way ride lasts one hour with a good connection, and costs �3430, but if you use the Japan Rail Pass, you need only to pay �300 for the Hakone-Tozan line.
Be aware that the JR East Rail Pass does not provide access to the Tokaido Shinkansen and to make use of this pass you will need to ride the regular Tokaido Main Line to Odawara. From Tokyo, a convenient choice that is valid with the JR East Pass is the "Odoriko" limited express train service. These trains have bigger windows and better seating than the regular commuter trains, and seat reservations can be made. As of March 2007, there are at least four daily runs, arriving in Odawara one hour later; there may also be additional runs on certain days. All trains make a pickup stop at Yokohama, while a few also stop at Shinagawa and Kawasaki stations.
You also have the option of boarding comfortable Green Car seats on regular JR commuter train runs. These seats are available on a first-come, first-serve basis, and you can purchase light snacks and drinks at your seat. You should purchase a Green Car fare ticket prior to boarding, which is done electronically using a SUICA card: