Clipper
Translink, when it is rolled out, will enable users to pay fares on any Bay Area public transit vehicle with debited cash, transfers or a prepaid passes (depending on the agency) using an RFID (touchless) smart card at no extra cost.
Deployment Schedule
From the official Tranlink site[1].
2006 (available now): AC Transit, Golden Gate Transit and Ferry, and Dumbarton Express
2008: Muni in trial
There's no timetable when the next transit agencies will come on line, but installation and testing of Translink is continuing at BART and Caltrain.