In addition to subway lines, electric commuter trains operated by Japan Railways (JR) run above ground. These are also color-coded, with fares beginning at ¥130. Buy your ticket the same as you would for the subway.
The Yamanote Line (green-colored coaches) is the best-known and most convenient JR line. It makes an oblong loop around the city, stopping at 29 stations along the way. In fact, you may want to take the Yamanote Line and stay on it for a roundup view of Tokyo; the entire trip takes about an hour, passing stations like Shinjuku, Tokyo, Harajuku, Akihabara, and Ueno on the way.
Another convenient JR line is the Chuo Line, whose coaches are orange-colored; it cuts across Tokyo between Shinjuku and Tokyo stations. The yellow-colored Sobu Line runs between Shinjuku and Akihabara and beyond to Chiba. Since the Yamanote, Chuo, and Sobu lines are rarely identified by their specific names at major stations, look for signs that say JR Lines.
If you think you'll be traveling by JR lines quite a bit, consider purchasing an IO Card, a prepaid card similar to the SF Metro Card which allows you to pass through automatic fare gates without having to purchase a separate ticket each time. These come in values of ¥3,000 and ¥5,000. Remember, however, that if you have a valid Japan Rail Pass, you can travel on JR trains in Tokyo for free.
For more information on JR lines and tickets, stop by a JR Information Center at Tokyo Station (Yaesu side) or Shinjuku Station (both the eastern and western sides). You can also call the JR's English-language telephone service at tel. 03/3423-0111.
TRANSFERS--You can transfer between subway lines without buying another ticket, and you can transfer between JR train lines on one ticket. However, your ticket or prepaid card does not allow a transfer between subway lines and JR train lines. You usually don't have to worry about this, though, because if you exit through a wicket and have to give up your ticket, you'll know you have to buy another one.
There are instances, however, when you pass through a ticket wicket to transfer between subway lines (for example, when you transfer from the Yurakucho Line to the Hibiya Line at Hibiya Station). In this case, simply show your ticket when you pass through the wicket. The general rule is that if your final destination and fare are posted above the ticket vending machines, you can travel all the way to your destination with only one ticket. But don't worry about this too much--the ticket collector will set you straight if you've made a miscalculation. Note, however, that if you pay too much for your ticket, the portion of the fare that's left unused is not refundable--so, again, the easiest thing to do is to buy the cheapest fare.