Must see areas/things to do in San Francisco for hackers?

I third Mountain View, and the computer history museum. Also, while you are there, check out Hacker Dojo. If you need a lift anywhere I live a block from the train station in MV and never mind a quick siteseeing tour.

In the city, check out Tech Shop if you have any maker inclinations.

If you're going to head to Mountain View, visit the Computer History Museum. It's nice to know from whence we all came.

Though the place makes me feel particularly old when I realize how much gear in the museum is stuff I've worked on in the past...

Union Square. Ride the trolley, and visit The Chancellor (of Sliders fame). Also, you can visit all the hot new startups on the Mission and in SoMA.

If you can, ride the CalTrain down to Mountain View. There are lots and lots of places to visit there, including the GooglePlex.