Word!

What type of stuff do you like to do regularly? That would help us tailor some suggestions.

Definitely book in SF (or close to it) if you can. The South Bay is nice, but there isn't as much to see out there (sorry, South Bay mateys).

Some stuff off the top of my head:

Tourist Day: You gotta see some of the landmarks right? Are you opposed to doing a bike ride? My favorite thing to do is bike riding down Fisherman's Wharf and over the Golden Gate Bridge and back. I'd start at the Ferry Building (cool shops here too), where there is a nice farmer's market on Saturdays, with nice local food. Then ride along Embarcadero through Fisherman's Wharf, past Crissy Field then over the Golden Gate Bridge and back. Along the way, you'll pass by tourist shops on Fisherman's Wharf, tons of seafood places, Ghiradelli Square, and some great views of the SF Bay. You can also hop on a ferry to Alcatraz while you're down here as well if you're into that.

Views of the City: If you have a car, definitely make your way up to Twin Peaks. There is a parking lot up there that offers a birds eye view of the entire city. Also, they just kicked off (yesterday, in fact) a light show exhibit on the Bay Bridge which will be around for a couple of years, so it'll be worth seeing while you're here:

Museums?: If you're into museums and whatnot, there are a bunch around the city. SF MOMA (they are closing soon for a remodel) is downtown, along with Yerba Buena and Contemporary Jewish Museum. De Young Museum (fine art) and Academy of Sciences (science museum with indoor rain forest) are right across from each other inside Golden Gate Park. You can see both museums, as well as Golden Gate Park in one shot, as well as see the Upper Sunset neighborhood nearby (Irving St) as well as Haight Street.

Go see some music. MTT is doing Mahler's Ninth at Davies Symphony Hall on the weekend that you're here. Catch a jazz show at SF Yoshi's, or one of the nearby smaller jazz clubs (the SF Yoshi's just opened a few years ago, the original one is across the bridge in Oakland). Not sure if there are any other bands you like, but there's tons of music venues around the city (I can expand further if this interests you)

Neighborhoods: Check out the local neighborhoods. Haight/Ashbury is pretty famous, and is lined with hippies and smoke shops. The Mission is the most eclectic neighborhood, with tons of hipsters and bars and trendy restaurants (probably my pick if I was coming from out of town) -- I'd stick toward the Valencia/Noe Valley side of the Mission. The Castro is the gay center of the city, and is definitely vibrant with bars and restaurants. Chinatown is obviously overrun with Chinese people. North Beach is like the Little Italy of the city, with tons of Italian restaurants, bars and strip clubs. Pacific Heights is full of upscale shops, as is Chestnut Street/Marina district.

Wine Country?: Northern California is known for it's wine country. You can journey about an hour north and hit up Napa/Sonoma/Russian Rivery Valley. Napa is probably more impressive of a region for out-of-town folks, because the wineries are more grand and catered toward visitors. While you're up here, you can hit up one of Thomas Keller's joints in Yountville (French Laundry, Ad Hoc, Bouchon Bakery), but there are lots of great restaurants up here (Mustards is a particular favorite of mine).

Anyway, not sure what else to suggest without knowing what you're into. If anything here sounds interesting, I can definitely expand further, or try to come up with more ideas.

Just know that San Jose is extremely boring.

Spend all weekend in SF. QuestHate has a great list of things; in terms of food, though, I'd book a nicer place now. Reservations will fill up like crazy this close to your trip for the nicer places.

+1 for SF. Questhate's list hits the highs. You'll Run out of time before you run out of things to see/do. Have a look at http://www.yelp.com and http://www.tripadvisor.com/ to see  if anything else grabs you. Depending on how geeky you are, if you have some time while you are in SV, a trip to Fry's Electronics (http://www.frys.com/ac/storelocator/index.jsp) if you've never been to one is always a fun experience, or a trip to The Computer History Museum (http://www.computerhistory.org/) if it fits in with your work schedule. for Fast-ish food, maybe Try In-N-Out if you haven't before. Some out of towners can't wait for their next "double-double Animal Style with Animal Fries" or other items on the "Secret Menu" http://en.wikipedia.org/wiki/In-N-Out_Burger_products.

Have Fun.

yep lots of nice record stores there. So far as food, if you are into the basics like burgers you definitely have to try St Johns Bar and Grill's burgers down on Lawrence expressway in the Sunnyvale area. Awesome stuff.