A common answer, which I agree with, is taking BART to the Embarcadero. See the Ferry building, check out the Bay Bridge light exhibit if you are there after sunset. Lots of good places to eat. The Exploratorium is an awesome hands-on science museum that just reopened in the area.

With that much time you could add Union Square or Golden Gate park. I'm partial to the park because I grew up near there. Lots to eat and good museums also.

It would help if we knew what you like to see in general when you travel.