So, I'm sure the real pro's of this awesome site will turn up in a minute and do the proper reccing thing, but in the mean time I just thought I'd mention an obvious one (that you've probably already read) but it's one of my favourites.

Sins of the Innocent (http://archiveofourown.org/works/212299)
http://archiveofourown.org/works/212299
Rating: Mature
Word Count: 83034
Dean has always known what he is and what it takes to control the demon inside of him. He and his brother were raised hunters, living isolated from the rest of society to protect both themselves and innocent civilians. When everything falls apart, they struggle to find their way in a world they don’t trust. They come to discover that they were never as alone as they thought and nothing is what it seems.

I'm not sure if it's what you're looking for, but poor Dean...he endures SO MUCH and it's all pretty much from John.

Also, here's a couple of good ones:

Words are Weapons (http://archiveofourown.org/works/1958328)
http://archiveofourown.org/works/1958328
Rating: Explicit
Word Count: 10988
Warning for Major Character Death.
Eighteen year old Dean and fourteen year old Sam live in the town of Lawrence, Kansas with their abusive father. Dean's always felt the need to protect his younger brother from the brutishness of their father. Dean's whole body was filled with bruises from his tyrant father. Sam was always John's favorite. Sam was the good son, who loved who he was supposed to love. When Dean meets Castiel there is an instant connection. What will the consequences of their forbidden love be? What will happen when Dean can't take it anymore?

In The Mourning (http://archiveofourown.org/works/2082678)
http://archiveofourown.org/works/2082678
Rating: Mature
Word Count: 5638
Dean Winchester is somehow still alive after yet another drug overdose, and Sammy puts his foot down and brings Dean to a treatment facility for Dean's various addictions. Dean hates it from the second he walks in the door, but a pair of startling blue eyes in process group makes Dean start to question everything he is. As Dean grows closer to the other patients, he finds himself falling in love with Castiel. But both Dean and Castiel are hiding huge secrets, secrets that threaten the safety of each other.

So Good, Baby Boy (http://archiveofourown.org/works/1089790)
http://archiveofourown.org/works/1089790
Rating: Explicit
Word Count: 17999
16 year old Dean and 12 year old Sam get jumped on their way home from school. Unable to save his boys, John is forced to watch as Dean is brutalized and sacrifices himself for his brother to the human monsters at his back. Will Dean be able to cope with the aftermath of his assault? Will any one be able to stop the abuse before it's too late? How will Sam handle seeing his idol damaged so badly?

The Scars Run Deep (http://archiveofourown.org/works/2125437)
http://archiveofourown.org/works/2125437
Rating: Explicit
Word Count: 7247
Dean was 15 the first time he put a razor to himself, it took 15 years for him to begin to heal. A suicide attempt, after Sam left for Stanford, left Bobby shaken, little did he know just how big a problem this was. Stemming from an abusive John Winchester, the problem persists long after John is out of the picture.

Protection
http://archiveofourown.org/works/589389
Rating: Mature
Word Count: 1266
Dean doesn't want Sammy to have the same childhood he did; he has to look after his little brother. In which John Winchester is an abusive asshole and Dean doesn't know what a healthy relationship with your family is supposed to look like.

The links don't seem to work so I added manual links.

Also, you can check out the Abusive John Winchester Tag on A03:
http://archiveofourown.org/tags/Abusive%20John%20Winchester/works

Hope You Enjoy!

Edited 2014-09-22 02:50 am (UTC)

Aaaaand here's some more, because now I've warmed to my theme.

Old Scar
http://archiveofourown.org/works/1761521
Rating: Explicit
Word Count: 5149
Season 8 Au-ish, where Dean suffers from the pain of an old wound. Sam thinks that he is the reason that Dean was hurt in the first place and he has beaten himself up for years.

Can't Rain All The Time
http://archiveofourown.org/works/1134025
Rating: Explicit
Word Count: 41397
The clock is ticking on Dean's deal, and as if things weren't tense enough between the Winchester boys, he doesn't react well when Sam wants to revisit their secret teenage romance. True to form, they push on with their latest hunt while the elephant in the corner of the room turns into more of a woolly mammoth. Following the trail of a missing witch and her elusive patron demon gets them stranded together in an abandoned house in the Maryland wilderness, where they've got no choice but to sort out their drama - except that house isn't so abandoned, and that demon isn't staying hidden anymore. Angst, drama and physical and emotional hurt/comfort, liberally sprinkled with sex.

A Little More Tequila, A Little Less Hunting
http://archiveofourown.org/works/1051949
Rating: Teen and Up
Word Count: 14209
What if Sam and Dean had had Max's childhood? What if John Winchester really had gone with "a little more tequila" and "a little less demon hunting"? Inspired by "Nightmare." AU except for various details from the Pilot. Lots of Young Sam and Dean in the form of flashbacks, and obviously NOT John Winchester friendly.

I think the specific story you're looking for is this one:

Winchester Family Angst (http://sarcastic-fi.livejournal.com/19987.html)
SUMMARY: AU: Sam wants to introduce his girlfriend Jess to his family. The annual Harvelle Roadhouse get-together seems like a good place to do this. But with Dean still dealing with abuse, Sam lying to Jess, and hunters all over the place maybe it wasn't such a good idea.

Unfortunately though, it was abandoned.