Caltrain is a commuter rail service that operates in San Francisco (4th and King), through San Mateo County and down to Santa Clara County (Gilroy). Started in 1987, and powered by diesel (though in the process of electrification). There is also a Baby Bullet service which stops at limited stations to cut down commute time. It has transfer stations at 4th and King to Muni (also conveniently located next to Telephone Park), Millbrae to BART (also to SFO), Mountain View to VTA, Santa Clara to Amtrak, and San Jose Diridon to ACE and Amtrak.
New projects include: the underground extension from downtown San Francisco to the future Transbay Terminal, Dumbarton Bridge rail to the East Bay, and a proposed extension to Monterey County.
Knights of Columbus! I just missed the train! Now I have to wait another hour to wait for the next one to arrive. DAMN YOU CALTRAIN!!!