1. Get a Clipper card, a debit farecard that works on almost all transit systems in the Bay Area. Ideally, order one onlineto be mailed to you (takes 5-7 business days), and you can immediately set up Autoload, which reloads your card from a credit card or bank account so you can “set and forget”. Unused value never expires (though you cannot get it back as cash). If you don’t have 5-7 days of lead time, you can buy this card at Walgreens drugstores anywhere in the Bay Area, or at the Muni vending machines in the underground stations at Embarcadero, Montgomery, Powell or Civic Center. Unfortunately you can’t yet buy them at the airports. Once you have the card, put some money on it at any Add Value machine in the underground stations or at any Walgreens. Both methods let you use credit cards or cash. When your trip is over, keep the card for your next visit. (You’ll surely want to come back.)
Various separate agencies run Bay Area transit, but the Clipper card works on all of them. BART runs fast trains that connect San Francisco, Oakland, Berkeley, and the outlying suburbs. Muni runs the buses, trolleys, and “Metro” streetcar/subways in SF. Other agencies run buses in other counties. Caltrain runs a commuter rail system from downtown SF (station is adjacent to AT&T Park, the baseball stadium) to San Jose which stops all along the Peninsula.
2. If you have a smart phone (iPhone, Android, …) bookmark NextBus.com, which provides real-time bus arrivals for most Bay Area agencies based on transceivers mounted in the buses. It uses GPS to detect where you are and give you departures of nearby buses, or you can select a specific route, stop and direction. You also may want the Embark iBART app, which has both schedule info and real-time arrivals for BART trains.
3. Use Google Maps (or the built-in Maps app on the iPhone) to get public transit directions between any two points. The route and connection info is accurate, but the specific connection times often aren’t because buses may be delayed during peak hours, etc. The ideal app would combine the directions from Google Maps with bus departure times from NextBus, but as far as I know that app doesn’t exist yet.
4. Become a member of Zipcar or CityCarShare, both of which have rent-by-the-hour stations all over the Bay Area. If you’re already a member, everything should just work. Zipcar has way more vehicles and pickup spots.
Tips on seeing specific things:
The best way to see the Golden Gate Bridge is to bike across, and take the ferry back from Sausalito or Tiburon. Bike rentals are available next to the Hyatt Embarcadero Center hotel at the Embarcadero BART station and various locations along the Embarcadero between the Ferry Building and Fishermans Wharf. The rentals include helmets, locks, and excellent maps. If you don’t want to bike the bridge, the next best way to see it is to get to the bridge plaza on Golden Gate Transit bus10 or 70, which is a lot faster than getting there on Muni since the GG Transit buses make very few stops in SF.
The Ferry Building (just outside Embaracadero BART station) was beautifully restored in the early 2000s and now hosts an urban-agriculture farmers market several days/evenings a week, at which all products must originate within 150 miles of the building. It is well worth a visit. Ferries do still sail from here; if the weather is nice, you can joyride the Alameda-Oakland Ferry, which makes a stop at Oakland Jack London Square and another in Alameda before returning to the Ferry Building (whole trip takes about an hour and you get great views of the Bay Bridge and the lay of the land). A nice “triangle schlep route” is to take the ferry from the Ferry Building to Alameda/Oakland, end up at Pier 39, walk over to Ghirardelli Square and cable-car back downtown from there.
The Castro is famous for being the gay epicenter of SF, but it's also just a terrifically vibrant neighborhood with some of the best-preserved examples of Victorian architecture, with many houses dating to before the turn of the 20th century. Get there by taking Muni Metro lines J, K, L, M.
SF has the US’s largest Chinatown, highlights of which include Waverly Place (Tin How temple dates back to Gold Rush days), Ross Alley (home of the tiny Golden Gate Fortune Cookie factory, where you can see them being handmade and eat them right off the production line), and the Vital Tea tasting room (sample a huge variety of traditional teas that will change your idea of what tea is).
Haight/Ashbury was the epicenter of the 1969 "Summer of Love" and still a neighborhood whose beatnik/hippie roots are very prominent. Get there by taking Muni bus #6 from downtown/Market Street.
Some of the best views of the city (in the late morning/early afternoon, before the fog rolls in) can be had from Diamond Heights/Twin Peaks and Lands End/the Cliff House out on the beach.
Have an outdoor lunch on nice day at The Ramp (about a mile south of AT&T Park) or Gordon Biersch (on the Embarcadero, under the Bay Bridge).
Locals tend to steer clear of Fishermans’ Wharf, but it does have those fascinating sea lions, and other things in its general vicinity are worth visiting, like the Musée Mécanique containing hundreds of really old (some from early 1900s) mechanical amusement devices, the USS Pampanito submarine, Fort Mason Park, the Maritime Museum, the recently-restored Crissy Field, and the Municipal Pier. Traffic is awful around there, so either bike there from the bike rental at Embarcadero, walk there from the Embarcadero BART (~20 minutes), or take the F-Market aboveground streetcar from in front of the Ferry Building.
There’s a fascinating collection of restored old ships and interpretive outdoor exhibits of SF’s maritime history at the Hyde Street Pier (just beyond Fishermans Wharf along the Embarcadero). You can also get there on Muni bus 19-Polk or 45-Stockton. Nearby is the lovely curving Municipal Pier (at the foot of Fort Mason Park, which has excellent views of the Golden Gate and Alcatraz). A further hike along the length of Crissy Field will take you right to the foot of the Golden Gate Bridge south anchorage and historic Fort Point, now open to the public, a fort/lookout that guarded the Golden Gate before invaders were able to drive into San Francisco over the bridge.
Outside of SF, Berkeley is well worth a visit, for both the campus and the vaguely funky Telegraph Avenue area just south of the campus’s Sather Gate. The best way to get there is to take BART to Downtown Berkeley station.
The best way to visit Golden Gate Park is Muni Metro N-Judah from downtown (runs along southern edge of park) or 44-O’Shaughnessy bus from our neighborhood (stops next to the Citibank right across from BART).
Dolores Park/Mission Dolores is the oldest original construction still standing in SF. You can reach it via Muni Metro J-Church or walking a few blocks from the 16th St./Mission BART station.