A good way to start to figure our how to get around the SF Bay Area is the Transit.511.org - Trip Planner.

Coming from San Francisco:

• You can get to Stanford via Caltrain that departs from 4th and King and 22nd Street. Getting of at the Palo Alto Caltrain Station you will have a pleasant 15 minute walk to the conference.  Please do observe that the first Caltrain sadly does not arrive in Palo Alto until just after 9 so you will be a little late.

From the East Bay:

• Bart connects to Caltrain at the Millbrae Station. Continue south towards Palo Alto.

Local Palo Alto Transport:

• The Shopping Express and Midnight Express shuttles will be running their regular schedules this weekend with minor detours due to the Amgen Tour of California.  You can find the schedules at http://transportation.stanford.edu/marguerite/MargueriteSched.shtml.  On Saturday and Sunday, the Midnight Express will not stop at the Oval. Riders should instead use the temporary stop at the southwest corner of Roth Way and Lomita Drive.
  
• On Sunday, the Marguerite Shopping Express will not stop at the Palo Alto Transit Center. Riders will be directed to a temporary stop at El Camino Real and Quarry Road. Please visit http://transportation.stanford.edu/marguerite/amgen for maps of these detours.