Recently, Passmo has taken over. It's a system exactly like Suica, except that ALL train lines (and even buses!) have been adapted to use it.
While this Passmo sounds great, I prefer to use Pasmo which actually exists in reality.
When it's said that they are "exactly like Suica" what should be pointed out is that, for Tokyo, Suica and Pasmo are functionally identical. If you already have a Suica card you need not change it for Pasmo. As well, though I haven't seen any documentation on it, use of the standard debit card Suica no longer deducts the standard 130JPY for JR (the lowest, 1 or 2 station, price) at the station of departure. I'm not sure if there is any inherent advantage to this (I haven't tried entering and leaving the same station yet); it just seems to be a side effect of being integrated with non-JR lines.
What's so great about Tokyo anyways....?!? :@
Hey, don't be so bitter, I hear they'll be installing/integrating Pasmo in Kansai, too. In a year or two!
Hahaha, get with the now!