I lived in Frisco for a couple of years. You should have a nice time there. Pier 39 is just a tourist trap - there's a bunch of shops and restaurants, but you're going to spend more money than you'd like, and overall it's not worth the effort if you're not in to that kind of thing. There are a bunch of harbor seals in the bay all around the pier and it STINKS, especially in the summer.
Definitely do a bay cruise on one of the dozen-ish boats that provide such things. Go to the Golden Gate bridge, and if you've got an hour or two to kill, walk across the bridge.
If you've got an afternoon or a whole day, and you're in to wine, you can't beat going to Napa or Sonoma. There are several tours that depart from the city, drive you up there, then drive you back.
Ghirardelli Square is all right, but touristy. Definitely do Alcatraz - I lived there and never went there.
You could walk along the Embarcadero or walk up the stairs from the Embarcadero to the top of Coit Hill and see the tower. You could catch the Metreon for movies/shopping/food. Get a sourdough sandwich while you're there - just about any place in town makes a good sandwich. I worked on Market and there were about a dozen within easy reach and they were all good.
Bring a jacket to San Fran. They have an odd climate, and often at that time of year it gets pretty cold. We froze our butts off at a Niners game one night in August.