1 week, 4 days where I’ll be busy and 3 full days for anything I want. Other than Saturday night, that’s for whiskey tasting.
West Coast leading 19 - 14!
As of this moment (9 March 2012, 18:50 PST), this thread is leading the nearby Things To Do In Fort Lauderdale thread, 19 posts (that’s not counting this one) to 14 posts. (With, I’m pretty sure, also a larger average number of suggestions listed per post too.)
You gon’ be busy!
ETA: Seriously: You need to think about whether you want to spend those 3 full days doing a whirlwind tour where you briefly touch on as many things as possible, or a more in-depth touring of just a few choice items. A LOT of the things mentioned here can easily be half-day or even full-day adventures!
(Og forbid you should end up spending a whole day just trying to get through the airport.)
Since the OP mentioned Oakland, I’d like to speak up for the food scene in that city. Some really great restaurants have opened in Oakland in the past several years, including:
Barlata Tapas Bar - I ate there tonight, and it was great!
Flora - I haven’t been there, but it has a good reputation.
Ozumo - High-end Japanese food.
Brown Sugar Kitchen - High-end soul food. Known for its chicken and waffles, but not limited to that by any means. The waffles are the best I’ve ever had - order one as a side dish even if you’re not getting chicken.
Pizzaiolo - The best pizza I’ve had in the Bay Area. They also have other Italian dishes. The place doesn’t have its own sign - look for the Dutch Boy Paint sign.
Boot and Shoe Service - Owned by the same people who run Pizzaiolo. A somewhat simpler and more informal place than Pizzaiolo, with less emphasis on pizza.
Tamarindo - Mexican small plates. Their food is more refined than at a typical Mexican restaurant.
Plum - Inventive menu. I hesitate to call it “California cuisine” for all that implies, but I can’t come up with a better name for it.
Heartily seconded. This takes you into the Marin Headlands, where there is a lot to see.
While you still have the car, drive up to Mt. Tamalpais for even more views.
The views from the Berkeley hills in the East Bay are also excellent if you have a chance. Drive up through the UC campus towards the Lawrence Hall of Science, then go past that to Grizzly Peak Blvd. and turn right onto it.
Take an interpretive walk in the Marin Headlands or Muir Woods. Interpretive Walks | Golden Gate National Parks Conservancy A sample: Search | Golden Gate National Parks Conservancy March 25, Muir Woods
At this time of year you have a chance of seeing salmon spawning, or ladybugs swarming on one of the fenceposts along the stream.
Or if you’re up for a real hike http://www.nps.gov/goga/parknews/upload/pa_spring2012.pdf (page 16)
Of course, you can visit the park areas without a guide.
The Musee Mecanique is free, but you have to put coins (usually a quarter each) into the machines (so bring a roll of quarters). I think it’s at Pier 45, which is three piers west of Pier 39 (which is a major tourist trap, complete with Hard Rock Cafe).
The Pinball Museum in Alameda has an entrance fee ($15 or $20, I think), but there is no charge to play any of the games.
You aren’t that far from the Sonoma and Napa Wine Valleys, although driving across the Golden Gate Bridge can be an adventure; the lanes are only 10 feet wide, and there is no barrier separating the two directions of traffic (as the two middle lanes change directions during the day based on the commute).
Also note that, if you do take a tour of Alcatraz, reportedly they are starting to get snarky about people asking about/searching for the “hidden areas” they see on the TV series.
(Note to Senegold: you can walk/bike across the Carquinez suspension bridge (just south of Vallejo) and also one of the two Benicia bridges (between Benicia and Martinez), if you consider those “in the area”.)
Most of my recommendations have been covered. The Trolley Museum is also free, and definitely worth visiting.
The Computer History Museum is awesome, especially if your experience with computers is pre-PC. They had a Difference Engine set up when I was there - I think it went back to England now. They have a working PDP-1, which I programmed in college. When I retire I will be so volunteering there.
There is also a nice Jewish Museum in San Francisco, which showed me, an ex-New Yorker, why we can’t good pastrami around here. Also second the Oakland Museum.
The Comic Museum has mostly strips from various times, which is fine but not as interesting if you are not interested in newspaper comics. I liked it but I can imagine some people being bored.
I was not impressed by the Exploratorium. Good for kids, but the Tech in San Jose is better for adults, depending on the exhibit of course.
Intel has a small, but free, museum in the lobby of the Noyce building of Santa Clara, though I haven’t been there since I worked there 15 years ago.
Even as New Yorker I say all the art museums are good, though you should check for interesting exhibits.
And I heartily second the Marin Headlands as a good place to go in good weather.
Well, he’s looking for adventure, right? Marin/Sonoma/Napa ARE thoroughly great areas for a visitor to go touring. But allow a FULL day (if not two) for it, if you really want to see a lot there. (Check out the Sonoma (City) “Valley of the Moon” drive, or the Peanuts museum in Santa Rosa.)
I didn’t know your could walk/bike across the Carquinez or Benicia bridges. I know one (or both?) have been completely re-built recently. Is the sidewalk new then?
ETA: And of course, Mr. Snarky-Kong, as soon as you get back home, the Teeming Millions will expect a full accounting of your adventures! With PICTURES!
Mr. Snarky_Kong, you’ve got a full smorgasbord of ideas here!
There are a lot of suggested places above that I haven’t seen. And I live about a 2 1/2 hour drive away from San Francisco. I’m bookmarking this thread, and I’m going to refer to it for a list of things that I should see.
All I can say is that when I lived there I drove over the bridge occasionally and never felt that there was much more risk than any other undivided 4-lane road.
You’ve been away a while. Now, all drivers and passengers must stop for TSA full-body scans, strip-searching, and occasional intimate groping. The traffic back-up get horrendous. Plan on getting to the Bridge 90 minutes early just to be sure. 
Same with the Caldecott Tunnels on 24.
Speaking of food, hit up Boudin’s and try some genuine sourdough. All my relatives that have moved away jealously buy up loaf after loaf when they visit.
Nava:
My only time in San Francisco and the surrounding area was also back in 2003. Wild coincidence if it was the same time. (Late January)
To the OP:
Alcatraz in San Francisco, the Jelly Belly factory in Fairfield, the Tech Museum and Winchester Mystery House in San Jose are the things we saw that were within an hour’s drive of San Francisco and recommend highly. We also rode a cable car and drove down Lombard Street for local flavor, and we enjoyed doing those things, though those don’t sound like they fit the OP’s question.
The rest of our vacation was spent in parts of northern California considerably farther from the area where you’ll be.
For bread I recommend Acme, which sells out of the Ferry Building Marketplace. They have several different types of sourdough, but my favorite is their walnut levain.
April I think. My team was visiting a bunch of factories; the company had wanted us to “go home” for the weekend, but I was visiting the LA location on Friday and the SF (well, across the bay) one on Monday with my boss, and his brother taught at Berkeley. Getting authorization to stay over in SF rather than flying cross-country twice in a single weekend wasn’t very difficult, for some reason. I loved it and would love a chance to go back for a longer vacation.
Hey, Snarky_Kong, are you in Oakland/S.F. this week or next week?
Needless to say, we all want a complete and detailed report of your adventures, and which of the many suggested places you went and what you saw and did there!