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Both Lyft and Uber operate at SFO–and are about $40 to the Stanford area. Pickup is fast and the drive is direct. Get the app for your phone and order. Taxis from the airport to Stanford-area should be about $80-$90. There is also a train (possible until about midnight, $10, but takes a transfer to Caltrain at Millbrae) http://www.bart.gov/guide/airport/index.aspx, and Super Shuttle: http://www.supershuttle.com/ (~$30)
Also consider Socialdrv (http://socialdrv.com/): An shared ride service specializing in airports. You can reserve online ahead, and the drive will track your arrival. It's pretty awesome.
There's also a SamTrans express bus (route KX) that runs roughly hourly between the airport and Palo Alto transit center (the bus/train station referred to above): fare $2.00 (03/2013). Takes just less than an hour. http://www.samtrans.com/schedulesandmaps/timetables.html Sadly, this very useful route no longer runs. (2015)
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