Trip to San Francisco... Things to do?

[Frinkenstein]

OOT,
I just arrived in San Francisco for a short course on Rock Mechanics and Rock Engineering. The course runs from Monday until Thursday 8am - 5pm. However, I am staying until Sunday to do some touristy stuff... My girlfriend is flying into town on Wednesday night to join me.

Things that are already on my list of things to do:
-Alcatraz
-Looking around Union Square (is there anything to do there besides shopping?
-A maximum of 2 art galleries of my girlfriend's choosing.

What else is a "must see" in San Francisco?

Thanks.