My short list of Must See's in SF and close surrounding areas.

Everyone mentioned Napa... that's a given.

1. Musee Mechanique.
Go there. Trust me. It's closing September 1st, and it's future is up in there air. It's a national treasure as far as i'm concerned. Hundreds of coin-operated automatic mechanical musical instruments and arcade games from the 1880's on. Simply amazing. While you are there you'll get to take in the Cliff House, the Sutro Baths, Ocean Beach, and the tip of Golden Gate Park... all within very close walking distance. An SF original for sure, that you won't see anywhere else on earth.

2. Twin Peaks overlook
The best view of the city, from the city. You can see all the bridges and an amazing overview of the city itself. On a clear day you can see the ocean, as well as across the city to the bay, Oakland, Berkeley, North to Marin, and South to San Jose. You also get a good tour of Castro on your way up if you take the Market St. Route. I take EVERYONE who's never been here there first. Here is a panorama i took from up there.

3. Marin Headlands
This is a good half day trip... could even be a 3 hour round trip if you want. It's awesome because you get to take in the Golden Gate Bridge from the best vantage point there is, as well as the rest of the bay, the Mouth of the bay including light house, and another amazing view of the city, Some old forts... i could go on and on. It's just over the Golden Gate, so it's close.Here is a shot from up there.

4. In the city... I'd stay away from Pier 39 just because it's such a tourist trap... with nothing you won't find elsewhere. Fishermans Wharf is another tourist trap, as is Ghiridelli (sp?) square. North Beach is pretty cool... tons of great food... and while you're there you can go up to Coit Tower for more amazing views. The Castro is always a good time if you want a little local flavor. There's so much... i'll stop here.
I like the non tourist off the beaten path stuff. Like... screw Lombard... that's not the real crookedest street. Here's the real one...

I've got tons more. Lemme know when your gonna be in the city and well go get dinner if you're interested. Email me.