Uh, Fisherman's Wharf is a a tourist trap. Some interesting stuff to see, but really stay somewhere else and wander over there on your own and spend a few hours at the Chocolate Factory going in and out the door to get the samples.
Sausolito is very cool as is the wine country. If you're in SF long enough to do Alcatraz, while touristy as heck, is pretty damned impressive.
When I visited, I booked one of those hop-on-hop-off bus tours and it was damned handy to get around town on. Feet tired? Hop on and ride around a while. Wanna see something? Hop off and wander around. Leave the car for the longer trips out of town, heck the wine tour bus wasn't bad either.
Golden Gate Park is beautiful and the museums there are excellent, well worth the trip. You just missed the King Tut exhibit at the de Young, so I'm not sure what they're doing there right now, but still worth the trip to see it.
I've had pretty good luck with Hotwire.com and if you're a member of Costco, etc they sometimes have deals through them.