Faults (http://www.fanfiction.net/s/3701621/1/Faults)
Summary: Stanford AU. For decades, scientists have been saying it's a matter of when, not if, the San Andreas Fault will falter again. When it does, CA will lie in ruins, millions of lives will be lost, and chaos will prevail. In 2004, those predictions came true.

In Case of Emergency (http://www.fanfiction.net/s/3954240/1/In_Case_of_Emergency)
Summary: Sam's away at college and both boys learn to cope without the other, but nothing is easy for a Winchester.

And also I would recommend cindy123 (http://www.fanfiction.net/u/1474733/cindy123) Third Brother verse where Sam and Dean have an older brother, the last story in it has Sam away at Stanford with John, Dean and their older brother going to get him because he was in the hospital. It's an awesome verse.

Revenge Not So Sweet (http://www.fanfiction.net/s/5052563/1/Revenge_Not_So_Sweet)

Oh and there's this one that has Sam still in Stanford but Dean's sick and he has to give him a transplant, so there is equal amounts of Hurt!Dean and Hurt!Sam

Faded (http://www.fanfiction.net/s/3596968/1/Faded)

And spn_littlebro has a tag in delicious about stories from Stanford Here (http://delicious.com/spn_littlebro/when%3DStanford)

And if you don't know spn_littlebro it's a rec'ing community for hurt!Sam and hurt!Jared so all stories are focused on that in some way.