Whenever anyone comes to visit us, this is our standard checklist of things to do and places to eat:
Alcatraz -- make sure you buy tickets about 4-6 weeks early, because they pretty much always sell out, year round.
Pier 39 -- this can be combined with Alcatraz, basically you walk around and buy some overpriced food and pay for really overpriced parking, doesn't take that long at all. I think in October the sea lions are there, they're cool. You also get really good views of Alcatraz from the end of the pier. Things to avoid around the Pier: the wax museum, totally not worth it.
Golden Gate Bridge -- You go, you get your picture taken in front of it, you maybe walk across it, it's pretty easy to park your car around the bridge, I have no idea how to get there using public transportation though.
Lombard Street -- You go, you get your picture taken in front of it, you maybe walk up and/or down it, if you have a car you should definitely drive down it. I honestly have no idea why anyone would want to live on, or near, this street since there are always tons of people around.
Muir Woods -- Really big trees, totally worth it. It can get really crowded (I mean you have to park 1-3 miles away crowded) on weekends and in the summer.
China Town -- Pretty much all the stores sell the same crap, but everyone has to go at least once, we've always just chosen a restaurant at random while there and I don't think any of them have ever been bad (except for service, that almost always sucks).
Golden Gate park -- I really like the Japanese gardens, it only takes an hour or two to walk through and it's really tranquil, there are also tons of other things to do in the park, and you can drive to the west end and end up at Ocean beach, which is quite a nice big beach.
Trolley car -- The most expensive public transportation in SF, we usually jumped on around China town but the ride is really short from China Town to the end of the line so I would find a different place to jump on and milk it for all it's worth since tickets are like $5-8 and I don't think it matters where you jump on, everyone pays the same price (it's been a while since we've taken anyone on the Trolley cars).
Food recommendations:
The Stinking Rose -- Everything is made from/with Garlic, even the ice cream. This place is touristy, but the food is pretty good. I really like the prime rib, and the short rib is good also. Not close to Bart, kind of close to Pier 39 if you have a car.
Umami Burger - They sell artisan hamburgers, if you like hamburgers, chances are you'll like them. Not close to Bart.
Taqueria Cancun -- This is without a doubt my absolute favorite Mexican restaurant in SF, I usually get an assortment of super tacos, people that get the burritos like them also. You can get here from 24th or 16th st Bart.
http://www.yelp.com/biz/taqueria-cancún-san-francisco-5
Soma Street Food Park -- Something for everyone at lunch, kind of dead during dinner (less people, less food trucks) on the weekdays, though I've heard dinner on the weekends is alright. 20 minute walk from 16th st Bart.
http://somastreatfoodpark.com/
Ike's Place sandwiches -- good sandwiches, it's semi-close to Dolores park, so you can grab a sandwich and walk the 3-4 blocks to the park to eat it. 20 minute walk from 16th st Bart in a different direction than Soma Street Food
http://ilikeikesplace.com/
Phat Philly -- I really like the California cheese steak from here. Easy 5 minute walk from 24th st Bart.
http://www.yelp.com/biz/phat-philly-san-francisco
Things we haven't been able to find:
A really good seafood restaurant, all the ones we've tried haven't been that great. The ones around Pier 39 are overpriced and I've never been blown away by the food.