Originally Posted by
joejones
JR has no service inside the Yamanote loop, so it's only useful for going around the city, not through the city.
Well, with the obvious exception of the Chuo/Sobu line, which is occasionally very handy.
All things considered, though, just go for a Pasmo -- it works everywhere and, for most travelers, the price difference is minimal or works in Pasmo's favor. You'll probably need one anyway for the other two days.