Getting there

Closest airports to fly into:
San Francisco (SFO)
San Jose (SJC) - often a bit cheaper than SFO.

Flights from Chicago O'Hare on American , Delta, Frontier, Jet Blue, Continental, US Air, Air Tran, and others.

Southwest has a sale going on now for midweek and late-week flights to SJC out of Midway. Reasonable Indianapolis fares available too.

Good fares frequently available on either American, Continental, Delta, and Air Tran from Indianapolis and Bloomington (BMI) for those coming from Champaign-Urbana. Sometimes you can find a surprisingly reasonable fare out of CMI too.

-> -> -> Quel surprise! American is having a sale now (9.15) from Champaign (CMI) or Bloomington (BMI) to SFO.
From/To CMI: Out on Wednesday for $134. Back on Monday for $154. $330 overall including tax (Even cheaper coming back Tuesday.)
From/to BMI: Out on Friday for $134. Back on Monday or Tuesday for $134. $310.80 overall including tax.

-> Also, American's sale has flights to SFO leaving on Friday from Indy and coming back Monday. A quite trim $260 including tax.

Fares to SF from other locals also on sale. Sale seat go quick, from what I understand.

-> -> JetBlue's sale has seats for less than $300 from JFK to San Jose Fri 10.1 - Mon 10.4 now (9.17).

Driving:
General directions from the north
General directions from the south
General directions from the east

Re: Rental cars
Available at SFO
Available at San Jose
Priceline is also great for car rentals if you're feeling lucky.

Public transport:
BART
Caltrain
SamTrans