K-Bell gave you some good advice on sights to see. Stay away from Fisherman's Wharf, it's a tourist trap. (Unless you're going to Scoma's to eat Cioppino, which is well worth the schlep to the Wharf - but once you're done eating, leave, because that's all that's worthwhile over there!) Golden Gate Park is MUCH more worthwhile, and has so many of the great spots in the City - the DeYoung museum, the Academy of Sciences, the Conservatory, the tea gardens... walk over to Park Chow for lunch or dinner... check out the Strybing Arboretum... SO much better than the Wharf!
We always direct friends and family toward The Handlery hotel. It's right on Union Square (coincidentally, where all of the best shopping in the City is, the trolleys, etc).
If you have a free night and enjoy blues music, I'd recommend going to Biscuits and Blues (just catty-corner from The Handlery). They always have great bands.
September is a great time to go to Napa and Sonoma for some wine tasting, as well - right in the middle of the harvest, so there's a lot to see and do. Napa is less than an hour from downtown SF.
Even if it's still hot where you live, remember weather in SF changes from minute to minute, so pack lots of layers! And comfy walking shoes, because walking is the best way to see the City!