I know there are free walking tours in San Francisco (http://www.sfcityguides.org/). My husband and I walked everywhere and rarely took any transportation as the city is a good size but we managed to get around fine walking. We spent about 7 hours a day just walking around on our own with our map. You can also pre-book a harbour boat tour for $19 as opposed to the $22 you'd pay when you got there: http://www.blueandgoldfleet.com
If it's your first time, I would recommend buying SF CityPasses. They get you into some fabulous museums, give you an unlimited pass for public transportation, come with great Pier 39 coupons and have other great features as well (they escape me at the moment - it's been awhile since I went). I hadn't ever been to SF before and used the CityPass as my gateway into learning about the city. Costco.com sells them cheaper than the CityPass website (but check to be sure if you're interested). Have a great time - and bring layering clothes. The temperature changes by the minute!
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