We are thinking about flying in and out of San Jose instead of San Francisco or Oakland because the airfares are cheaper. Is there any sort of public transportation available to the San Jose airport from the San Francisco area? If not, any idea of what cab fare might cost?

Sorry, I don't know the way to San Jose.

Caltrain. Once you get off the train (I think it is a Santa Clara stop) there is a free shuttle that takes you to the San Jose airport. We usually take a cab to Caltrain on 4th and then take the train all the way down. We have done it--it is even eaiser for us then BART to the Oakland airport. When you return from the San Jose airport on the train there are always a bunch of cabs out front of the train station (day & night) to take you to your house.

I'd recommend the Caltrain too. When you arrive in SJC, you can take a shuttle or a cab to the Caltrain station. Then in SF you can take a cab or a bus from the Caltrain station to your hotel.

Go to the SJC web site and check out the ground transportation section to see all your options.

Here's a link to the San Jose airport ground transportation. Pick the means you feel most comfortable with.
I would recommend the door-to-door shuttles. Give them a call and check them out. Some of them have vouchers. When we left SF to SFO, some of the passangers had prepaid vouchers from, I believe, Expedia. Check it out. (b)

http://www.sjc.org/travelers/ground_trans.html

Your best bet is Caltrain. Take the #10 VTA/SJC Flyer bus which stop in front of each terminal and get off at the Santa Clara Caltrain Station. A cab to San Francisco from San Jose would be about $150.

Thanks everyone, this is great! Sounds like Caltrain is exactly what I am looking for,