511.org combines all local transit (BART, AC Transit and more) in one easy place, so you can search for the best route and know how long it will take before even leaving the house.

You can even download the information to your PDA (Treo, Blackberry, etc.). You can sign up for four free days of transit through Sparetheair.org, which also has programs through large employers. Ask your work about incentives for alternatives to driving including telecommuting part-time — there are tax benefits for businesses and there may be benefits for you in addition to saving gas money. Also check out Casual Carpool for sites in the East Bay to hop a ride into San Francisco.