I've been a few times and can share what I loved.
In the city, check out Hayes valley. There's a cool outdoor beer garden there, and it's right next to a liquid nitrogen ice cream place. It's a good spot to waste an afternoon/evening.
We did Alcatraz... it's touristy, but well done.
I've also walked up to Coit tower a few times. If you like hiking, this is as good as it gets in a city.
The seafood down by the water is good too - we ran into bad luck and all the good spots seemed closed though. Don't go for the big touristy places that have cheap crap food though. Find the little hole in the wall places just off the main drags.
If you have some time to go outside the city, Muir Woods is alright. It's not a real hike, more like a walk. Point Reyes is gorgeous - I loved it there. Big Sur is a good drive away but is one of the most beautiful spots in the world.