As is common, I disagree with Roja. The "tourist ghetto" of Fisherman's Wharf/Pier 39 and 41 can be a lot of fun. See the seals. Go down the Embarcadero - you can see the "Fog City Diner" (you may remember it from the Mike Myers movie "So I Married an Ax Murderer"). Hit the financial district - the Sony Metreon. Grab a copy of the SF Weekly and the Guardian - free papers like the Village Voice but thicker and better. See Ghiardelli Square. Snag a deal (they're there, but you have to find them) at the Levi Strauss factory. Go to the Haight and people watch. Visit Golden Gate park (there's supposedly the ghost of a police officer that roams there). Go to the Exploratorium - a LOT of fun. Visit the Presidio - make sure you see the military cemetery. Walk from the Presidio across the Golden Gate bridge to Sausalito and back (and bring a coat - the water is always 48 degrees, and, no matter how sunny, it always seems to be cloudly/foggy when you're on the bridge proper). For sure, get some sushi and some dim sum. Near the Bay Bridge and Tunnel, you can see the cargo loaders that inspired George Lucas to create the AT-AT walkers for The Empire Strikes Back. Oh, and, the coup de gras - get tickets the day before for Alcatraz. You won't regret it.
SF is a hell of a ride.