A friend of mine who grew up in San Francisco sent me the following e-mail about recommendations when I went out there. I cut and pasted his recs. I actually enjoyed Alcatraz too.
1. Fort Point/Golden Gate Bridge - Fort Point is a civil war fort that is actually underneath the Golden Gate Bridge. You can tour it and from inside you can look up at the bottom of the bridge. Also, it is cool to watch the fisherman and surfers and you can hike up the hill and across the bridge if you want to walk across the bridge.
2. Golden Gate Park - there are all sorts of cool things including, but not limited to, the arboretum, Japanese tea garden, museum, aquarium .... I used to go there as a kid to see the Pink Floyd laser light show. I believe it is still showing.
3. If you are renting a car I would suggest driving north up the coast. Cool features are the Marin Headlands - there is a marine wildlife rescue center there, the redwoods in Muir Woods, and Point Reyes National Seashore.
4. I was always a big fan of hanging out in North Beach in the city. It is the old Italian neighborhood that borders Chinatown. There are a lot of cool restaurants, bars, and stores. I am a big fan of Caffe Puccini for coffee and City Lights Bookstore is well known as being a haven for beatniks. Also, it is right next to Broadway. So if you have any interest in visiting the same strip club that Clint Eastwood goes to in "dirty harry," you are all good. You can also walk from there up Telegraph Hill to Coit tower. I've never been up the tower, but it has a great view.
5. Ghiradelli Square - it is a huge mega tourist trap, but the ice cream parlor underneath is well worth the wait. Also, it is across the street from the apartment building from which the mob boss plummets to his death in "magnum force."
My big advice is that if you don't mind taking public transportation, you would be well suited to save your rental car money for when you plan on exploring outside the city. You can take the bus or subway from place to place and even walk through a lot of it.
For eating:
1. Dim Sum - for this I have a couple of different suggestions. If you are in North Beach and want a quick meal to go that you can walk to the park and eat (or even up Coit Tower) go to Louie's Dim Sum at 1242 Stockton Street.
http://www.yelp.com/biz/louies-dim-sum-san-francisco-2 <http://http//www.yelp.com/biz/louies-dim-sum-san-francisco-2> If you want the sit down experience there is no better place than Ton Kiang on Geary Blvd
http://www.yelp.com/biz/ton-kiang-san-francisco And in case you were wondering, you must get dim sum.
2. For a damn fine burrito I like La Taqueria at 2889 Mission Street.
http://www.yelp.com/biz/la-taqueria-san-francisco-2 It used to be something of a dicey neighborhood but now it is far more safe. Nonetheless, go for lunch not dinner. Also good, and featured on Man versus Food is taqueria la cumbre - same neighborhood and good, just not my personal favorite.
http://www.yelp.com/biz/taqueria-la-cumbre-san-francisco Their burritos are the size of newborn children.
3. Italian - the original U.S. Restaurant at 515 Columbus Ave. It is very traditional italian american and it is the place I grew up going to
http://www.yelp.com/biz/original-us-restaurant-san-francisco
4. Meat - the House of Prime Rib. Tony Bourdain went there in his visit to San Francisco and suggested it was the type of place he would happily die. Enough said.
http://houseofprimerib.net/home.html
5. Drinks -
The Buena Vista - on Hyde Street across from Ghirardelli Square it is where Irish Coffee was invented.
http://www.yelp.com/biz/buena-vista-cafe-san-francisco It was also featured in the Lucille Ball classic "yours, mine, and ours."
The Saloon - its the oldest operating bar in the city, a total dive, and cool as shit. The music can actually be very much quality and it has a small cover. Also, it has the strangest bathroom I have ever encountered in my life
http://www.yelp.com/biz/the-saloon-san-francisco
Harry Denton's Starlight Room - if you want to feel like your in the 50s and spend way too much money, this is a great choice:
http://www.harrydenton.com/
Alternatively, you can hit up the Top of the Mark - I have no idea if the food is worth a damn, but it has some of the best views you will ever see, it is historical, and sometimes you want to class it up. I once made the mistake of starting at the Saloon and ending at the top of the mark. You should do it the other way.
http://www.intercontinentalmarkhopkins.com/top_of_the_mark/ You may also remember it from the hit television show M.A.S.H. Captain Honeycutt spoke of it often.
Enjoy.
