San Francisco is a beautiful, world class city. There are numerous museums, places of nature beautiful, great food, and well known tourist spots. You could easily spend several weeks exploring San Francisco and only scratch the surface. The SF City Pass can be a good deal. The greater SF bay area has more Michelin stars than NYC… for a list of them check out sf-eaters site. If I was going to try to stuff highlights of San Francisco into a few days I would recommend the following:
South of Market (SOMA) – Mostly
Take CalTrain to the city. Check out SF Modern Art. Thee are plenty of lunch options around the museum. My favorite places are the Samovar Tea House and InSitu which is inside SF-Moma. The Metreon Food Court is popular with some. If folks are worn out, head home, otherwise consider explore Chinatown and take a cable car ride.
Golden Gate Park
Start by exploring the Golden Gate Req Area, Muir Woods (great redwoods), Golden Gate Bridge, Golden Gate Park. In the park there are a number of museums such a California Academy of Sciences (wonderful for younger kids).
Pier 39 & Waterfront
The Pier itself is a tourist track and isn’t worth a lot of time, but it does provide access to the ferries which can take you to Alcatraz, Angel Island, etc.