There will be opportunities to use your Rail Passes in Tokyo even though they may not save you a lot of money. Just walking through the manned counter to access the Yamanote Line or other JR trains without having to buy tickets is a help. The Yamanote is not expensive at all but standing in line at the ticket machine can be a pain at times.

Just be sure when you use it that the train or station you are entering is JR. The Rail Pass is not valid on private lines or the subways.