Never is a Promise by magicletters - Dean tries to hold things together so he and Sam can survive life with an abusive father.
http://magicletters.livejournal.com/10138.html#cutid1

Abandoned by Rafikiven - Set immediately after Sam leaves for Stanford. John and Dean aren’t handling it well.
http://rafikiven.livejournal.com/10503.html

Silent Treatment by alwayspromised - The 'silent treatment' is a form of social control. It consists of ignoring a particular individual, neither speaking to them nor responding to their words. Pre-series
http://alwayspromised.livejournal.com/8906.html

Shelter Me by Maz Kazama - At the time, Sam hadn't even wanted an older brother and John had wanted another son for all the wrong reasons. Over the years, Sam came to accept his unwanted, unloved big brother as one of the family and John...just didn't.
http://www.fanfiction.net/s/4597078/1/Shelter_Me

Here you go: have some mean!John> and bad father!John (http://www.diigo.com/user/redfoxrose/bad-father!John)

Though they probably overlap some. (http://www.diigo.com/user/redfoxrose/mean!John)

Sins of the innocent
http://archiveofourown.org/works/212299/chapters/317961

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 hope you don't mind self-rec's, but I have several bad!evil!mean! John stories. A lot of them are Wincest with graphic sex, but not every one of them. They are all situations where Sam is the one being physically abused.

http://hellesofbelles.livejournal.com/45379.html#cutid1

http://hellesofbelles.livejournal.com/44226.html

http://hellesofbelles.livejournal.com/31938.html

http://hellesofbelles.livejournal.com/34603.html#cutid1

I really thought I had more than this...

A Split In the Skin (http://archiveofourown.org/works/178300) by callisto

Wolfpack series (http://tabaqui.livejournal.com/113022.html) by tabaqui
- wincest

These three are AU and all are Cas/Dean and all have abusive John, though not as the main component:

Off by Heart (http://archiveofourown.org/works/236627/chapters/362608) by mytimehaspassed
- The day you drop out of high school, you hollow out your English textbook and fill the void with dime bags. Croat verse AU. (AKA SAD AS HELL)

We Three Kings (part one of the Three Kings verse) by cosmic medusa
- Cas understands, early on, that falling in love with Dean meant adopting Sam. He didn't count on the devasation and addiction that would follow him though. The ones dealing with John are here (http://cosmic-medusa.livejournal.com/20009.html) and here (http://cosmic-medusa.livejournal.com/16873.html).

12 Steps (http://gedry.livejournal.com/tag/12%20steps) by gedry
- The 12 Steps tell you to keep it simple, but Dean Winchester has never been good at keeping anything simple.