I've posted several itineraries of recent SFO trips on the Ca and the West board.
Question I have - San Jose is not nearly as public transportation friendly as SFO and they are a 45-60 minute drive apart. Are you planning to hop back and forth between them and how much time are you spending in the area.
I'm headed to San Jose this weekend with my DD, we are going to head to the Tech Museum and to the Rosicrucian Museum. If there is no snow over the Sierras. I grew up in San Jose and we go a couple of times a year. We have spent about 11 days in SFO this year also. We love the city.
If it were me, I would attend the conference in San Jose and have a car there if you are planning on sight seeing etc. while in San Jose. A nice drive to Big Basin Redwoods State Park
http://www.bigbasin.org/to see some redwoods, or perhaps out to Santa Cruz
http://www.explorer1.com/santacruz/attractions.htmfor dinner on the wharf or even just to catch an amazing sunset on West. Cliff Drive.
In SFO, ditch the car. Use Muni, cabs, BART and cable cars. Parking in SFO is spendy, plan on $25-35 per day and that includes at most hotels.
My favorite place to stay is a bit off of the beaten path, in the somewhat quieter community of Cow Hollow/Marina Dist. I like the Travellodge Golden Gate on Lombard and Steiner. Not fancy by any means, but it is clean and close to shops, restaurants and Muni stops. It does have free parking as a perk. We usually arrive, park and never take the car out until we depart.
What not to miss really depends on your tastes. For me it would be a walking tour of the Golden Gate Bridge via City Guides (free tours)
http://www.sfcityguides.org/
I also love china town, I love the sights, smells and restaurants as well as the atmosphere and if you are really adventurous, get off of Grant St. which is the main "tourist" drag, go up a block to Stockton and explore the local markets. The fish/poultry markets are incredible to see. SFO has super strict health codes, it is safe to eat anywhere, you may not like it but it won't harm you so give it a try. Our favorite restaurant is the Washington St. Bakery and Restaurant on Washington Street just below Grant St.
http://www.washingtonbakerysf.com/
Cable car riding IMO is a must, I like the California line, far less crowded with tourists and it goes up and over Nob Hill, past beautiful hotels (Mark Hopkins and the Fairmont) as well as Grace Cathedral on the corner of Taylor St and many beautiful homes.
http://www.sfcablecar.com/routes.html
We always buy a Muni pass that is good for unlimited use of buses, trolleys and cable cars. FYI a muni pass is not good on BART, that is a separate entity.
The "Impressionist: Masterpieces from the Musee D'Orsay" currently on display at the DeYoung Museum is really beautiful and IMO worth the visit, we saw the first phase in July and will be returning in January to see the second phase.
http://deyoung.famsf.org/
Then of course there is the tourist mecca of Fishermans Wharf which IMO is worth skipping, but if you have never been you might want to swing on by, have a clam chowder bread bowl so you can say you did and say hi to the sea lions.
http://www.fishermanswharf.org/
Something else I would not miss would be an Alcatraz tour and I highly suggest you try for the one that is at night! Its amazing.
http://www.alcatrazcruises.com/
The Walt Disney Family Museum is really quite an extensive collection and I suggest you allow at least 4 hours.
http://disney.go.com/disneyatoz/familymuseum/index.html
Also refer to Yelp.com for great neighborhood restaurant reviews.
Again there are several of these threads over on the Calif & the west board. Check them out and enjoy SFO it really is a beautiful city. Also refer to Yelp.com for great neighborhood restaurant reviews.