San Francisco - what to do there
Temperature in San Francisco is cool - days start foggy, normally, below 60 F, and tend up to the mid 70's on a good day. Dress casually and take a sweater or light jacket. The climate is the same throughout the year, with slightly more rain November to March. Outside of the city, both north and south, temperatures are higher, and there isn't any fog. Shorts are always appropriate.
From the airport to the city is about 40 minutes, and the best option is to take one of the minivans that go to the downtown hotels - about $14 one-way. San Francisco International Airport is being rebuilt (2001), and there may be a BART link in the near future. If you aren't going to the city, you need to hire a car, although there is a CalTrain link a short bus ride away that is an interesting way of getting to San Jose.
East of the Civic Center and Van Ness Avenue, and north of Market, there is nothing dangerous. The Tenderloin is the area around the Civic Center: stay out unless you know what you are doing. Other areas should be treated like a normal American city - with care, because you don't know the warning signals. South of the airport is mostly OK - avoid East Palo Alto, and parts of San Jose.
Take a day out to walk around San Francisco, and an extra day for either the 49 Mile Drive, a trip to Fry's, or a tour through the Napa Valley. I use these for de-jetlagging.
If you are on foot:
For shopping, look in the Union Square area (Macy's, FAO Schwartz, Virgin - DVDs, CDs). There is a new Sony cinema at the Metreon Center, which is at the Yerba Buena Gardens (4th and Mission?), by the Moscone Center. This always has a good range of films showing, and other exhibits as well as a food court.
Take a cable car from Union Square to Fishermans Wharf. The cable car museum is supposed to be good, and it is on the route. It is a lot easier to get on going in this direction than in the reverse.
Go to Fishermans Wharf, but be aware that it is very touristy and crowded. Look at the tourist tat on Pier 39, and in Ghirardelli Square. Probably worth eating a clam chowder in a sourdough bread bowl from Boudins (branches all over San Francisco); I do this for breakfast, before the crowds arrive (or stores open). Go see the sea lions at the end of the pier. Consider taking a look at the sailing ships and submarine on the next pier along. At the back of Fishermans Wharf, near Tower Records, the Marriott and Columbus Ave is a decent bookstore with coffee shop (Barnes & Noble). Most of the restaurants here aren't very good, but Lou's (I think) used to have good music - it may still. The sea food restaurant in Ghiradelli Square is also rated, and is much cheaper for lunch than dinner - it might be called Culletto's. DO NOT go to the Imax on the Pier, the film is awful.
If you can, walk the length of Columbus back to the Union Square area; the cable car stop is really crowded. Taxis can also be hard to find, but may be easier to pick up if you stand outside one of the hotels. Columbus passes though North Beach and the edge of Chinatown into the Financial District. Brandy Ho's is a reasonable chinese on Columbus, on the edge of Chinatown - it isn't the full-on Chinatown experience, but the food is good. In North Beach, see City Lights bookshop and Vesuvio: stop and have a beer/espresso. This is where the beat poets hung out. Tosca's is a plesant opera oriented cafe. You can detour from here to go up Telegraph Hill to Coit Tower, which is better than you might think.
In the Financial District are the TransAmerica Pyramid, and the Bank of America building. There is an express elavator to the top of one of these, with a bar. You can watch sunset from it, but get there early, because every one else wants to.
There is also a reasonable shopping centre (the Embarcadero Centre), which has a good Chinese dim sum restaurant (the Harbour Village) at the Embarcadero (East) end of it. The Sharper Image store is nearby, and Staceys on Market is one of the better book stores.
The Redwood Room at the Clift Hotel is superb - art deco and martinis. Have a drink at the top of the Fremont Hotel for the night-time view.
To visit Alcatraz, you have to book a couple of weeks ahead; you might be able to get a midweek booking if you book the previous week. So I don't bother. But you can get the ferry from Fishermans Wharf to see the Bay, and stop at Sausalito or Tiburon. Recommended is to book dinner at Guaymas (Mexican restaurant), which is at the ferry terminal in Tiburon; but the last ferry leaves about 7pm, so book for an early dinner. You can also book a seaplane tour around the bay; apparently there is a place in Sausalito that will give a cheapish flying lesson in one.
On the subject of dinner, Mortons at Powell/Post (Union Square) may be worth a visit; it is a Chicago style steak house, and expensive. The best bit is the menu, bu the food is good as well. Booking is a good idea. Another decent place is Fog City Diner, just off the Embarcadero. I should also mention Tommy's Mexican Joint, on Geary just north of the Golden Gate Park. This is a good Mexican, with a bar that specialises in tequila.
This may sound strange, but I often buy a Jamba juice for dinner/breakfast. There are several branches around the Bay Area, including one in the basement of Macy's at Union Square.
FYI: Liz rates the tights you can buy in Victoria's Secret as almost indestructible. Union Square.
Take the 49 Mile Drive. It is marked on all the maps, and signposted by a blue and white gulls head sign; pick it up starting on Market. This is the best scenic drive around the city you can do. You get to see Coit Tower, Fishermans Wharf, Union Square, the Embarcadero, the Exploratorium, the Presidio, the Golden Gate Bridge, Haight/Ashbury, the Golden Gate Park, Chinatown, etc. Liz liked the camera obscura at Cliff House.
There are a couple of steep streets that you need a car to appreciate: the twisty one is Lombard, and the really steep one is Filbert.
If you have time, it is probably worth stopping at the Exploratorium.
Drive across the Golden Gate Bridge to Marin, and stop at Stinson Beach. The first turn off on the right immediately over the bridge is popular. You get to see some redwoods, etc. It is also quite popular to walk across the bridge.
Go to Palo Alto, see the university and coffee shops and book shops, and visit Frys.
Visit Berkeley (much the same): the book stores are on Telegraph Avenue.
Go shopping: there is a high class shopping mall near Palo Alto on the highway called Stanford Shopping Center.
Napa Valley. Drive to Napa, along the valley to Callistoga. Have lunch at the Callistoga Inn. Make sure that you do tours of Mondavi (good tour and tasting); Sterling (great cable car, lousy wine); and Clos Pegase (weird 'modern' architecture, interesting wines). Tastings mostly start at 10am, and cost money.
Marin. Muir Woods and Mount Tamalpais: walking in the redwoods. Stinson Beach: a beach. Liz likes to visit the cheese factory (on the road from Point Reyes to Petaluma), and stay at the Point Reyes Seashore Lodge in Olema. If you go to Point Reyes Seashore Park in the right season, you can whale watch from the lighthouse. But it is always foggy. Anywhere on the route up to Mendocino is interesting, with lots of pleasant small inns and B&Bs, many of which serve good food as well.
Highway One. The great drive is to take 1 south from San Francisco, through Monterey and Carmel, past Big Sur, and finish at San Simeon. You can stay the night down there, and do a tour of Hearst Castle. Recommended. The Monterey Bay Aquarium is good.
Yosemite, Lake Tahoe, and the Gold Rush country are all (even longer) trips.
See here for links to San Francisco attractions.