lived there most of my life (but no longer). What a wonderful place!
In no particular order:
1. walking around Chinatown and North Beach neighborhoods ... then eat at Cafe Sport (Believe it or not, the waiter is your friend, do not piss him off, tip 30%, and you may have some of the best Italian food ever).
2. check out the gnarly Ocean Beach surf (many world class surfers live nearby) and after the fog gets into your bones, grab a cappuccino at Java Beach (LaPlaya and Judah, at the N-Judah Muni turnaround).
3. visit to the Stanford (35mi south) and Berkeley (15 mi across Bay, accessible via BART, too) campuses.
4. hike from Muir Woods to Stinson Beach via Bootjack and Steep Ravine trails...roundtrip plan a day including the beach. as the name suggests there is elevation, but not too bad. Hope you like scenery!
5. hiking (flat) thru the SF Zen Center's Green Gulch Farm in Muir Beach....beautiful hills, organic gardening, and Zen Meditation. You may still be able to arrange overnights.
6. Good Vibes:
Sweetwater Music Hall, Mill Valley (a tradition back to '60s, Bob Weir is one of the new owners)
Terrapin Crossroads, San Rafael (Phil Lesh's new club, and he's playing later this month)
WHOA!