Spectacular Views

Twin Peaks - best place to get an overall view of the city. Best accessed by car, on the routes of many bus tour companies.
[Twin Peaks Blvd]
[Map]

Marin Headlands - Go for a walk up to the old gun turrets for views of Golden Gate Bridge. Best accessed by car, on the routes of many bus tour companies.
[Conzelman Rd and McCullogh Rd, Marin County]
[Map]

Walk from Crissy Field to Golden Gate bridge - Start at Marina Blvd and Mason St and head West
[Map]

Hire bikes and ride from Crissy Field, up over the Golden Gate bridge, down into Sausilito for coffee/lunch, and take bikes on the ferry back to the city. Don't be fooled if the sun is shining - bring layers and wrap up warm, it gets chilly on that bridge at the best of times. Look where you're going and watch out for high-speed bike traffic on the Western bike lane at weekends, all other times proceed with caution on Eastern sidewalk where you'll be mingling with pedestrians.
[Bike hire]
[Sausilito visitor info]

Golf

Harding Park Golf Course - 99 Harding Rd, San Francisco
Presidio Golf Course - 300 Finley Rd, San Francisco

Shopping

Union Square [Post and Stockton] - There's a coffee shop/bar on the square where you can have a rest. Also, see the Westfield Mall /Emporium [Market St. and Powell], nip into John Foley's Irish House for lunch [O'Farrell and Powell]. See also, the glass elevators.
[Map]

Fine Wine and Dining

Lunch at Cliff House - followed by walk down to the caves below. Clam Chowder recommended.
[1090 Point Lobos Ave]
[Map]

World Famous Napa Valley - wine tasting, spas and outlets. (Saturdays not recommended, traffic is crazy.)
[Napa visitor info]

Top of the Mark [Mason and California] - Cocktails on the top floor of the famed Mark Hopkins Intercontinental Hotel. ($10 for a Cocktail, used to bankrupt me in my efforts to impress girls up there when the sun was setting, but sure aren't you boys getting a good exchange rate?) A bit of a walk around nearby Grace Cathedral is something you could do in the daytime and highly recommended.
[Taylor and California].
[Map of Nob Hill]
[Grace Cathedral]
[Top of the Mark]

Columbus Ave, North Beach - Italian restaurants galore with the Transamerica Pyramid looming over all at the bottom of the street. Famous landmarks include the Vesuvio bar and next door the City Lights Bookstore, open late most nights.
[Columbus and Broadway]
[Map]
[Vesuvio]
[City Lights]

Quirks and Oddities

The glass elevators where you can look down on Union Square - Best not to go in 'en masse' if you're not guests at the hotel. In small groups, go into the Westin St Francis Hotel and walk through to the back and to the right to the elevators. Get in, press 29, turn around, and hold on to your stomach.
[Powell and Geary]
[Website]

Haight Ashbury - This famous intersection was the epicenter of the 1960s hippie movement. Today full of unique cafes, bars, music shops, and stores that sell all manner of beads, pipes, hookahs, and other hippie paraphanalia.
[Haight and Ashbury]
[Map]
[Wikipedia entry]

Lombard St. - The 'world's crookedest street' runs one block from Hyde to Leavenworth. On the cable car line that runs from Powell to Fisherman's Wharf.
[Hyde and Leavenworth]
[Map]
[Article]
[Wikipedia entry]

Other Activities

Fisherman's Wharf is good for getting to Alcatraz, assuming you've booked your Alcatraz tour far enough in advance that it's not sold out. The Ripley's Believe it or Not Museum is worth seeing, and there are some good eating houses on the waterfront. Shopping for anything but cheap souvenirs here is not recommended since it's a bit of a tourist trap.
[Embarcadero and Pier 45]
[Map]
[Alcatraz tours]
[Ripley's]

Academy of Science if you're interested in aquarium/rain forest/penguins etc.
[55 Music Concourse Dr, Golden Gate Park]
[Map]
[Website]

If you need somewhere to kick a ball around informally, we recommend Marina Green as a place to knock about and warm up, do a bit of training with the Golden Gate Bridge as a backdrop. Gets chilly after 5pm.
[Marina Blvd and Fillmore]
[Map]
[Article]

Other Tips

Climate
San Francisco has a unique 'micro climate.' It can be ten degrees warmer as soon as you go north of the Golden Gate Bridge or south of Highway 380. In the city it is notoriously changeable, so wear layers that you can peel off later, and never set off without a warm jacket no matter how warm it seems. Even crossing the street can see a noticeable difference as you move in or out of the shade behind the buildings.

Earthquakes
California is in an earthquake zone. If you feel a tremor, it will likely be over by the time you have felt it. If shaking continues, get out of the building if it is convenient and away from the path of any falling glass. Failing that, get under a desk, table, or other solid fitting, Failing that, get under a doorway. Most older buildings have been seismically retrofitted, more modern buildings are built to withstand shocks.