I have some rec's that sort of fit what your asking for- and I noticed no one had replied so these might work for you.

Muffy Morrigan has a story where the boys run across Sam's friends in Vegas - and Dean leaves them to visit and while he is on a hunt- Sam gets hurt.
http://www.fanfiction.net/s/3740162/1/Last_Plane_Out
sequel
http://www.fanfiction.net/s/3796116/1/Homeward_Bound

And Abni has a story that takes place right after Skin where Dean notices a scar on Sam he hasn't seen before. It leads to a reveal about a hunt during his Stanford time.
http://www.fanfiction.net/s/3873442/1/Hitting_Walls_and_Getting_Scars
sequel
http://www.fanfiction.net/s/4103075/1/Picking_Up_the_Pieces
sequel
http://www.fanfiction.net/s/4174568/1/A_Curse_Between_Us
And she has this story-
http://www.fanfiction.net/s/4158699/1/The_Howling -summary-
While Sam is away at Stanford, Dean sets out on a werewolf hunt on his own. The hunt doesn't go as planned and Dean meets with more than one surprise along the way. HurtSam, hurtDean, not deathfic. Co-written by Manavie.

BlueEyeDemonLiz has a great piece about Sam's Stanford time that includes a hidden hunt.
http://www.fanfiction.net/s/4101298/1/Stanford_and_Sam
sequel Dean's pov
http://www.fanfiction.net/s/4140977/1/Sense_of_Duty

Wow lots of stories. Thank you so much! I', looking forward to reading them.

Shadow.