Just got back from 6 days in San Fransisco and had a great time. There is a lot to do and we got everything we really wanted to see in.
Some notes:
The airport was nice, modern and easy to navigate, not being huge helps with this.
Cable cars are handy midweek/midday in November, come Saturday you wait a long time, same probably goes for peak tourist season.
We rented a condo for the week instead of a hotel, it was cheaper than any decent hotel in the area (we stayed in Nob Hill), had a very comfy king size bed and a kitchen. A good option to consider if you go.
Fisherman's Wharf is something to see for a few hours but beyond one afternoon we had no desire to go back.
Alcatraz was cool.
We got City Pass's
http://www.citypass.com/san-francisco which were awesome,
Alcatraz, 2 museums, the Aquarium and transit for 7 days was well worth it.
Lots of walking up/down hill, good running shoes are an asset.
Went to Scala's at Union Square for the g/f's birthday, she loved it, mission accomplished. With drinks and tip it was $130 meal for 2. Glad I had a reservation as even on a Thursday in November walk ins were being given times 2 hours later.
Union Square has lots of shopping, but really the prices are similar to here so if you're looking for a deal it's not the greatest.
Didn't have a bad meal the whole time, we stumbled on a little Deli/Cafe called Jonas on Hyde (on the corner of Hyde and Vallejo) on our way to Fisherman's Wharf that had the best sandwiches I think I've ever eaten.