Sutro Project / BART
The 5th most-used rapid transit system in the country BART provides transport between and among San Francisco (including the airport) and the East Bay. Consisting of four partially overlapping lines that run about every 15 minutes, BART goes pumpkin around midnight. Bay Area transit is sparse late at night (eg, slow hourly transbay MUNI service), but it's never too late to make a new friend :)
Bikes are allowed except during commute hours - current details here.
Website: http://www.bart.gov/schedules/index.aspx
Wikipedia: http://en.wikipedia.org/wiki/Bay_Area_Rapid_Transit
