3 hours is not long enough to go to the City and back with TSA security and all the other potential delays.
If you can exit the airport, then SF is about 1hr roundtrip. Union square for shopping, Embarcadero and fisherman's wharf for quick bites. Golden gate bridge is always inspiring. Or head south to Stanford and visit the Rodin garden. It's free. There's so much to see in the bay area. Three hours isn't a lot of time considering the traveling time, so most likely can only choose 1 stop before returning to the airport.
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