http://511.org/511.org provides comprehensive, integrated travel help - plan your public transit trip, check highway traffic conditions and lots more
http://www.bart.gov/Bay Area Rapid Transit is a regional subway system serving San Francisco, the East Bay and the northern Peninsula to San Francisco Airport
http://www.sfmta.comSan Francisco's MUNI provides bus, rail, cable car and antique trolley service throughout that city
http://www.actransit.org/AC Transit provides bus service to and from San Francisco and throughout Alameda and Western Contra Costa counties.
http://www.goldengate.org/Golden Gate Transit serves the North Bay with bus and ferry service within the North Bay and connecting to San Francisco
http://www.caltrain.com/Cal Train provides rail service between San Francisco and San Jose, including shuttles to San Francisco and San Jose airports
http://www.nextbus.com/"Next Bus" provides up-to-the-minute information on when the next ferry, rail or bus will arrive at your location. Amazing.
http://www.sfgate.com/travel/resources/airports/A handy visitor's guide to all three airports: Oakland, San Francisco and San Jose
http://www.blueandgoldfleet.com/Blue and Gold Ferry provides ferry service between San Francisco and Sausalito, Tiburon, Angel Island, Vallejo, and Oakland & Alameda
http://www.baylinkferry.com/Baylink provides ferry service between San Francisco and Vallejo
http://www.watertransit.org/The future of Bay Area public transit is happening on the water - check it out! Plus links to all Bay Area water travel!
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2008/11/26/BA1S14C7Q7.DTLNew ferryboats going into Bay Area service that run at 85 percent lower emissions than required by the Environmental Protection Agency.