Alcatraz is def. fun if you are into that thing. You could always pop over to Oakland and dodge some bullets. If you are willing to make the mad dash through Oaktown Berkley is a pretty cool town. Lots of cool stores and dirty hippies.
Just watched Anthony Bourdain's The Layover about San Fran and was thinking it would be cool to do the shit he does, stays out the tourist areas. Watch the show. Was there a week but stuck working in a ship yard, but had time to take the ferry, i get say I saw a bunch of shit, and ferry goes in a big loop and you end up back where you started and it was cheap.
If you're into wine tasting, Napa Valley is pretty close, and driving a few hours north or south on Highway 1 along the coast is pretty cool... north maybe a little better unless you want to see Monterey/Pebble Beach/Santa Cruz (which is south). If you go south you can also check out the giant redwoods at Big Basin State Park... that's a must for some people which I don't really understand, but then again I see redwood trees every day.
Sausaulito was pretty cool the last time I went (to back up Blazin's suggestion), but that was ten years ago. If you're there through the following Sunday, the 49ers are playing the Lions at home.
Joe Derosa is at the Punch Line pretty much that whole week (at least the 12th-15th). I would definitely go to that show if I were down there.
Couple of notes from my Facebook from let year that I just looked up:
Zushi puzzle, best susi in city.
Irish bank-cool Irish place.
Buena vista-birthplace of Irish coffee. Good brunch.
If you are into Kerouac and the beat writers checkout the beat museum, city lights bookstore, and vesuvios bar. Pretty cool spots.
Coit tower was cool. Nice view and cook wpa era murals.
.I forget the name but if you like Bogart the bar from the malteese falcon is there with the actuak falcon.
Also there is a word of mouth speakeasy that I wrote the name down at home.