* The United States of Jensen (http://archiveofourown.org/works/514829): Jared needs a new place to live, and fast. Salvation comes in the form of a cute redhead named Danneel in his English class. Living in a huge spacious house with four other roommates seems like an ideal solution, but trouble has always found itself around Jared Padalecki, and this time is no different. He's had his whole live planned since he started University, but it looks like all it's going take is one man to knock it all down. // Jensen Ackles has been trying to fit in with everybody else for as long as he could remember. Broken from actions so horrible that he's blocked them from his mind, he lives in a world where the broken pieces of his self fight for control. He's managed to keep everybody he loves at a distance for all his life, but all that's about to change.
* Sam I Am (https://www.fanfiction.net/s/11208142/1/Sam-I-Am): (NOTE: This is a different one than the one recc'd above) Sam gets kidnapped by people determined to "save" him and the other special kids by making them use their powers for "good." The Sam that Dean and John rescue is shattered mentally and emotionally - the only way to keep himself from becoming the monster they want him to be.
* There's a Hell of a Universe Next Door (http://archiveofourown.org/works/905265): The curtains were pulled open again when Dean came awake and the light was fainter than when he‘d crawled into bed, but it was still too much. Still too invasive. And all the noise in his head, all the fear and that clawing sense of wrongness was back. The wind was blowing through that hole in his soul again and Dean felt his eyes water with it. “No,” he moaned, turning his face into his blanket. “Sam,” he whispered, holding the name to him like it would save him. “Sam.”
A few that might fit the bill
* Sam I Am (https://www.fanfiction.net/s/11208142/1/Sam-I-Am): (NOTE: This is a different one than the one recc'd above) Sam gets kidnapped by people determined to "save" him and the other special kids by making them use their powers for "good." The Sam that Dean and John rescue is shattered mentally and emotionally - the only way to keep himself from becoming the monster they want him to be.
* There's a Hell of a Universe Next Door (http://archiveofourown.org/works/905265): The curtains were pulled open again when Dean came awake and the light was fainter than when he‘d crawled into bed, but it was still too much. Still too invasive. And all the noise in his head, all the fear and that clawing sense of wrongness was back. The wind was blowing through that hole in his soul again and Dean felt his eyes water with it. “No,” he moaned, turning his face into his blanket. “Sam,” he whispered, holding the name to him like it would save him. “Sam.”