Excellent posting, Hawaldar.

Transportation

Bay Area Rapid Transit (BART)

• East Bay and North Bay are well connected through the Bay Area Rapid Transit (BART). 
• Both SFO and OAK are conveniently located near BART stations (have to take a short shuttle ride from OAK); you should have no problems getting to your accommodations when you arrive.
• Getting to San Francisco is just as easy. Hop on to the BART and you're there.
• The only limitations of the BART are that it doesn't go very far south. Millbrae is the last stop and you'd have to take buses there on.
• http://www.bart.gov (see route map below)

San Francisco Cable Cars

• Excellent way to get around the city.
• Runs on California, Powell, Hyde, Jackson, Washington, Mason, Columbus, and Taylor.
• Head east on the California line and you'll hit Embarcadero, which is basically where the Piers are.
  
• http://www.sfcablecar.com (see route map below)

CalTrain

• The CalTrain connects SF to Silicon Valley.
  
• You'll want to take this if you want to see Stanford or various company campuses, including but limited to Google, Cisco, HP, Apple, etc.
• You might even catch something at the Shoreline Amphitheater if you're lucky.
• http://www.caltrain.com (see route map below)

Valley Transportation Authority (VTA)

• These are buses that service mostly Silicon Valley and East Bay.
• They take up time but they'll get you where you want to go.
• http://www.vta.org (Here's the map: http://www.vta.org/schedules/pdf/system_map.pdf)

Hope this helps. Good luck and have fun, all!