Absolutely agree. If it hasn't already been pointed out, the prepaid Suica card can be used for virtually any transportation option in and around Tokyo - and other large cities - but also for many other small purchases such as at convenience and other stores and some vending machines. You put some money on the card at the beginning and can reload it if needed later. When you are ready to leave Japan, you can cash it in for a refund of un-expended money less a small deposit. Or, as I did with Kyoto bus/subway passes before the IC cards came out, you could just keep the card as an inexpensive souvenir. The Suica is a very good "go-with" to supplement your Rail Pass.

http://www.jreast.co.jp/e/pass/suica.html

If you haven't already done so, you might want to pick up a good guide book that has a subway map, as well as a train line map, for Tokyo. The subway lines look like a pile of spaghetti but color coding helps. It can be beneficial to research possible routes the night before to at least know which lines go to your destination. For example, I usually use the subway to get to Ryogoku for the sumo stadium, which is right next to the Edo-Tokyo Museum and also right next to the subway station. On the other hand, if I am going from Akihabara (Electric Town) to Ryogoku, I would use the JR train line and use my Rail Pass. It is complicated but if you have a map to look at it makes a lot more sense.