I have not been to SF, but I am considering train trips on coast:
Travel by Train in the San Francisco Bay Area and Northern California | Amtrak.
It looks like by train could do round trip also to San Diego, in couple of days.

Another thing I have thought about is the Anchor Brewery, but it looks like need advance booking for tour (months):
http://www.anchorbrewing.com/brewery/tours
.
Napa valley tour could be interesting to some people.
.
I myself would probably visit Stanford also, and I'd try to get a print of "Agassiz in the concrete" of which there are several views.
Scroll about half way down to figure 4 to see what its about:http://quake06.stanford.edu/centennial/tour/stop3.html
(Walking tour of Stanford)