You have to see the seals at the warf, they are so awesome! I also really liked the Japanese Tea Garden (in the Golden Gate Park). Alcatraz was a lot of fun too.
Ah… San Francisco… one of my very favorite places to go.
Calistoga is awesome… as are the vineyards. I loved Salsalito as well.
As for the city - twin peaks was great… and there’s an area I believe called the Mission that had an awesome taqueria!
If I think of the name, I will email it to you.
You guys have fun!!!!
Take the time to drive up to Twin Peaks. (Way at the top of Market Street) The view is amazing night or day, if it’s clear! Oh, it’s romantic too!
I don’t know where you are staying, but a great spot for drinks is at the top of the Marriot at Union Square (another GREAT view)
And don’t miss Chinatown! I would try to get across the Golden Gate to Sausalito too! It’s wonderful, and some great waterfront dining!
(I’m excited for you! Can you tell?)
Man, I’m so jealous! I love San Francisco.
One of my favorites is The Blue Lamp, a little blues places downtown. I also loved Golden Gate Park.
Palace of Fine Arts. Beautiful place! So jealous. I’ve only been to SF once and didn’t have near enough time there.
Oh! There’s also a nighttime tour of Alcatraz. By lantern light. Spoookkkeeee.....
if you can swing a trip over to salsalito...it’s such a quant little town! also a drive down the coast to carmel is awesome too! everything that was mentioned in the other comments was on my list too! try a bowl of soup (or chili) in a sour dough bread bowl is yummy!
The Exploratorium is pretty cool, but it’s immense… it will take some time.
Enjoy.
Really you’ve got the bridge and chocolate covered! I’d say you’re good to go! Have fun 
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Golden Gate Park is lovely—especially the Japanese Tea Gardens. When my wife and I were there for our honeymoon, though, I think we enjoyed just walking around the city as much as anything else. It’s a very pedestrian-friendly city; we practically walked it end to end in a matter of three days.
Alcatraz was kinda fun, but I didn’t think it was exactly a must-see.
Oh, and you should probably hit Chinatown, too—just to get the whole tourist thing out of your system.
Have a fun trip!