SF and Silicon Valley are relatively standard cities/areas (but the overall, Bay Area environment is fantastic). I don't think you'll find anything particularly special about San Francisco: it's a nice, cultured city, but you've already seen plenty of those.

As diego mentioned, Silicon Valley is about doing, so see the do-ers and the do-ers hangouts:

    * Visit google's campus in Mountain View (cab ride from Caltrain);
    * Visit DogPatch Labs in SF (15 minute walk from Caltrain);
    * Visit RocketSpace in SF  (15 minute walk from Caltrain);
    * Visit Hacker Dojo in Mountain View (10 minute walk from Caltrain);
    * Walk around Stanford's campus (5 min walk from Caltrain);
    * Grab coffee at Coupa Cafe or lunch at University Cafe
      in Palo Alto (5 minute walk from Caltrain);
    * Don't visit Facebook (it's a boring campus).

If you're an avid reader of Hacker News, seeing some of these places might provide some helpful context for the stories you read.

Obviously, if you're going to visit these places or others, drop another story on HN with places + times and I'm sure folks will try to greet you.