eracode: One time we were there we did a road-trip of a week or so - an anti-clockwise circuit - south through San Jose > Yosemite > circumnavigated Lake Tahoe > Sacramento > over to the Napa Valley then back to SF. Calistoga and St Helena in the Napa are really lovely places.
We just totally winged-it for accommodation each day - using booking.com on the fly from the car - but that may not work so well during peak vacation time.
Did something similar when I was there in 1995.
I had gone to a user group meeting in Mountain View (centre of Silicon Valley and might even had visited a building that existed on the site where Google now lives!) and had a 'free' day at the end of a busy week visiting various IT companies and local sites.
Hired a car, drove over the Golden Gate Bridge, up to Napa Valley then back via Berkeley and the Oakland Bay Bridge. A long drive with plenty to see and probably the best route as the reverse direction would have meant paying road tolls to travel over the bridges. I don't know if this is still true.
Re-visited San Francisco area as part of our Round-the-World holiday in 1998 with my wife. We also visit New Zealand for the first time of this time as part of this trip.