Here are a few places I always enjoy stopping in to see what's new --
The Cartoon Art Museum:
http://www.cartoonart.org/
Fort Point (right under the Golden Gate Bridge):
http://www.nps.gov/fopo/
Fort Mason:
http://www.fortmason.org/index.shtml
Hyde Street Pier:
http://www.nps.gov/safr/
The Presidio:
http://www.nps.gov/archive/prsf/home.htm
Note: Building 104 on the Main Post is under construction as the future home of the Walt Disney Family Museum. It's not open yet, but hopefully sometime in 2009 if all goes to plan. I've seen some of the plans and this will be a "don't miss".
CityPass San Francisco is the best deal I've seen. It includes a Seven-Day MUNI Pass which covers Cable Cars, Streetcars, Light Rail and buses. With Cable Cars at $5 a ride, this is a great money saver. Here's the full blurb from their web site:
"San Francisco CityPass includes five attraction admission tickets, a seven-day MUNI & Cable Car Passport, and saves you nearly half the price. CityPass bundles tickets to the most popular San Francisco attractions in a pocket-size booklet, along with attraction information, transportation directions, best times to visit, a map, special offers, and enticing destination suggestions from the pages of
National Geographic Traveler, the most widely read magazine for inquisitive travelers.
All CityPass attractions are accessible via MUNIs world famous cable cars and light rail: the de Young Museum and Legion of Honor, Aquarium of the Bay, SF Museum of Modern Art, and Blue & Gold Fleet Bay Cruise Adventure for spectacular views of Golden Gate Bridge, Marin hills, Alcatraz Island and the city. An Option Ticket gives you a choice between the Exploratorium OR Asian Art Museum. You have nine leisurely days from the day of first use to enjoy admission to each attraction once, and will avoid most ticket lines.
Discount and offer coupons invite you to save on other aspects of San Francisco culture: Choose a Blazing Saddles bicycle tour or GoCars little yellow GPS-guided car tour; shop Bloomingdales; take the Boudin Museum and Bakery Tour for a whiff of authentic sourdough; get a Pier 39 Fun Pack, sample a treat from Sees Candies; and get 2-for-1 admission to AT&T Park Tour at the home of the San Francisco Giants."
http://www.citypass.com/city/sanfrancisco.html
If you're looking for dining or drinking, my choices are:
The Buena Vista - Home of the Irish Coffee, right across the street from the Hyde Street Cable Car turn around.
http://www.thebuenavista.com/
The Beach Chalet - Great food and beer brewed on site on the Beach!
http://www.beachchalet.com/
The Garden Court at the Palace Hotel - History and fine meals, too. Pricey but worth it.
http://www.gardencourt-restaurant.com/
Also check out Maxfields with it's original Maxfield Parrish "Pied Piper" mural:
http://www.maxfields-restaurant.com/
Looking for a bit of Sam Spade? Try John's Grill, mentioned in the Dashiel Hammet novel, "The Maltese Falcon":
http://www.bestofsanfrancisco.net/johnsgrill.htm
Looking for some Tiki fun and food? Hukilau is it!
http://www.dahukilau.com/restaurants/sanfran.html
If you just want to graze? Check out the Ferry Building's shops and markets. Lots of good stuff here.
http://www.ferrybuildingmarketplace.com/
That's a good start! Enjoy.