From another thread I posted to about the same subject:
Don't miss the
Alcatraz tour...get your tickets early. Check out the
Musee Mecanique and tour the WWII submarine
USS Pampanito...both down near Fisherman's Wharf. Try riding the
Cable Cars too...the POWELL-HYDE line has the best views and the CALIFORNIA line is the least crowded. The
Cable Car Museum is really interesting too. Head up to
Twin Peaks for a fantastic 360° view of the City. Have a drink at the
Top of the Mark on Nob Hill. The
Disney Museum in the Presideo is pretty cool. It's not just about Disneyland, but more about Walt's life & career. For a little culture, check out the
DeYoung Museum in Golden Gate Park. The
Exploritorium is big fun for kids of all ages. Walk across the
Golden Gate Bridge.
Driving around SF is a total PITA and trying to park a car in the downtown area is nearly impossible...use public transit if you can. And bring some warm clothes...summer weather in SF can still be quite chilly, especially in the evenings.
This is what Anthony Bourdain would do in SF:
What to Do in San Francisco