there is No Fortunate Son (http://nocturniquette1.livejournal.com/tag/no%20fortunate%20son) by nocturniquette1.

The Comfort of Brothers (http://disturbinglynic.livejournal.com/121392.html)
Dean takes care of Sam after John abuses him.

Daddy, Please, No (http://samlikescock.livejournal.com/45275.html)
After Mary's death, John is very lonely, and he can't help but notice how attracted he is to Sam (who is eight). So, feeling absolutely disgusted with himself, John attempts to drink his feelings away. But that doesn't help; only makes them stronger, and harder to control. One night, while he's drunk out of his mind, he goes into Sam's room and starts touching him. And once he's started, he does it every night, his actions getting bolder until he finally rapes Sam (who is now eleven). After the rape, Sam becomes anti-social, and jumpy. He won't let anyone but John touch him (only because he's scared to flinch away from John). Not even Dean. And Dean noticed it, and goes to investigate, trying to get Sam to open up to him. And when he doesn't, he scopes out his room at night, finally catching John in the act. Once John's been caught, Dean takes Sam and runs to Bobby's house, explaining the whole thing to the older hunter, so when John comes to retrieve his boys, Bobby tells him to get off his property before he gives him a third hole. Over the years, Sam develops an obsession with Dean because he was the one who saved him from their father.

Don't Say a Word (https://www.fanfiction.net/s/4304684/1/Dont_Say_a_Word)
Henrickson's smart-ass comment reveals a surprising truth Sam didn't want known.

Replacement
It was John's way of dealing. It was Sam's secret he knew never to tell. Wee!chesters. Based off of authoressnebula's Don't Say A Word.

Red (http://wincest.livejournal.com/1047953.html)
What really made Sam decide to go to Stanford.

Mother Mary Comes to Me (http://phantisma.livejournal.com/210924.html)
Sam sometimes reminds John of his mother. When John sees more than a resemblance, he lets himself believe something that can't possibly be true. Sam pays the price.

xxx

and a few more .....

The Truth is Revealed! (https://www.fanfiction.net/s/5774467/1/The_Truth_is_Revealed)
Episode Tag to Devil's Trap. Alternate ending for this episode. The demon-john reveals some interesting facts about Sam's childhood.

Sin's a Curse and the Cure Is Worse (http://mya-rofki.livejournal.com/1247.html)
A story in which John catches Sam and Dean together and loses it, violently.

One Tape, So Many Lies (https://www.fanfiction.net/s/5599335/1/One_Tape_So_Many_Lies)
Dean finds a video tape that will change his and his brother's lives forever.

Please read the warnings on all the fics & i hope there's something that suits you

xxx

One of my all time favorites
http://www.sinful-desire.org/archive/viewstory.php?sid=2326&warning=5
This is slash

hehe. that's the same one I recc'ed. :)

Great minds think alike! LOL

Hmmm, doesn't fit exactly, but maybe :

http://spnkink-meme.livejournal.com/70931.html?thread=23941395&#t23941395