If you are visiting more of Japan then grab a Japan Rail Pass. This can be used on JR lines in Tokyo such as the Yamanote loop line. When I went I used it all the time to get around the city, which saved significantly on travel. It is only worth getting though if you are going to be travelling beyond the city, otherwise it's rather pricey.
Available in Japan at major railway stations for various time periods (eg 7 days, or a month).
Updates
First a correction, then an update.You must buy the Japan Rail Pass outside Japan. Your travel agent gives you a voucher, which you can exchange for a pass at major airports or train stations around Japan. You cannot expect to come to Japan and just buy a Rail Pass.
Don't bother buying one unless you plan to travel at least as far as Kyoto and back, because single tickets will be cheaper. (None of these silly time-sensitive price discrepancies on Japanese trains: the tickets cost the same no matter when you buy them.)
Now for the update: The Tokyo-Yokohama area now has its own equivalent of the Oyster Card, called either Pasmo or Suica, depending on who issues it, and it's good on JR Trains, private rail lines, the Metro, and city buses. It covers almost all public conveyances within an area about 50 miles by 50 miles, and you can buy it and top it off in increments of ¥1,000.
If you're traveling around Japan a lot, get the Rail Pass, though. It's such a good deal (for foreign tourists only) that Japanese people nearly weep with envy when you tell them about it.
The Japan Rail Pass certainly is a great way to travel round the country. Buy it before you go (get it online at www.accessjapan.co.uk, and lots of other useful info besides). One other point - you need to make sure you're stamped as a bona fide tourist ('temporary visitor' - the normal entry status for tourism, valid for a 90-day stay) in your passport when you arrive at Japanese immigration. What you actually get when you buy the Rail Pass is an 'Exchange Order': you can present this at main railway stations in Japan and start the Pass whenever you like... and it's valid for 7, 14 or 21 days continuously from that date.
Oh, and one last thing... travelling with the Rail Pass, you don't use the automatic ticket barriers at stations. You show your Pass to station staff and pass through a manual gate.
More info (and stuff about that Suica card thing too) from www.accessjapan.co.uk.
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