John/Dean stories had been written prior to the airing of Devil's Trap but the pairing became more popular after due to the chemistry between Dean and the possessed John.
Writers tend to focus on Dean's devotion and obedience to his father, combined with John's inability to express his emotions. Stories range from those focusing on the eroticism of the power dynamic, through to those where the relationship is purely abusive.
The John/Dean pairing is a lot less common than Sam/Dean mainly because many people do not like reading stories around intergenerational incest - the power imbalance is difficult for some people to get past. For others, of course, it's a positive advantage.
Additionally there simply isn't as much canon. While the boys' relationship with John is an important theme of the show, he's made relatively few appearances. John Winchester also isn't necessarily the most popular character in Supernatural, with some fans seeing him as an abusive father. Also some people don't find John Winchester attractive, but there's obviously something wrong with them.
During the LJ Strikethrough 2007, when there was concern over journals and communities containing incestuous material being deleted, the main Fanfiction community for John-centric incest fic, called "Daddycest" was moved from Livejournal to Journalfen on 15 August 2007. The community became inactive by the end of 2007. John/Dean fic continued to be posted on other fic communities on Livejournal.
- John/Dean stories tagged as part of the Supernatural Fic Link Archive.
- daddycest - A community for John/Dean, John/Sam and John/Dean/Sam fic on Journal fen - inactive since 2007.
- papawinchester - John-centric Livejournal community. Slash is locked for members only.
- jwinchester - A livejournal community centering around John Winchester.
- spndaddys-boy - A slash fanfic community for John & Dean Winchester.
See fic headers for warnings and ratings.
This list was started in 2006, when fandom was small. Obviously the number of fics in these categories now is huge. To find more recent examples visit the links above or see : Rec Communities.
Feel free to add your fic to the list!
A New Sort Of Animal by jobincityslacka
A Season In Hell by lilmissfury
Acceptance by Shorts
Adrenaline by xantissa
2006-0713 All That Stands Between Us by ellipsisblack
And then there were two by angstslashhope
A Night in Early June by Siset
Anything To Keep Sammy Safe by wilwarin1
As if We'd Never Met by thatotherperv
Beautiful Fucked-Up Man by lostdreamer56 (friends-locked entry)
Bed of Roses by lilmissfury
2006-08-23 Beyond All Recognition by olivia j.h.
Bittersweet Reunion by darkestangel
Black by sosoru
Bombshell by Derry
Break by bloodkisses
Burning by pixel
Come to Papa by lilmissfury
Curiosity by sylph_ironlight
Daddy's Boy by lilmissfury
Dark Shroud of Love by missyjack
Day Spa by derryderrydown
Deliverance by Shorts
Dirty by bloodkisses
Dirty Creature by flannelmistress
Down In My Soul to Stay by ebolacrisis
Echoes by missyjack
Every Now And Then I Fall Apart by lilmissfury
Fall From Grace by Shorts
2007-04-14 Familiar Admonishments by teand
Feel For Faith by lilmissfury
Hand Me Down Old Shoes by lilmissfury
He Never Said Goodbye by Shorts
Holy Water by lilmissfury
In the Air Tonight by lilmissfury
In The Dark by xantissa
In Vino Veritas by Morgan
Jealousy by lilmissfury
http://www.sinful-desire.org/archive/viewstory.php?sid=2343 January 24th) By JOhnsgurl
Life Without Sam by Nephthys
Like broken heroes by missyjack
Liminal by angstslashhope
Look beneath the floorboards (for the secrets I have hid) by ebolacrisis
My temples are burning by bloodkisses
Nightmares Series by darkestangel, Aelfsidene & Siset
No Longer The Little Soldier by Shorts
No Retreat, No Surrender by Shorts
Not Exactly the Bradys by Morgan
Not Strong Enough For This by kali_sama
Nothing Else Matters by lilmissfury
Paying Attention by sosoru
Peace When You Are Done by rosereddawn(=lacerta)
Precipitate by angstslashhope
Prelude by angstslashhope
Regrets by Siset
Revelations by Shorts
Sacrifice by Shorts
Shaky Ground by damerel
Single Father, Part-Time Mother, Full-Time Lover by lilmissfury
Suck You Dry by Derry
Sweet Child of Mine by la_folle_allure
Sweet Dreams and Blue by lilmissfury
Temptation by bloodkisses
That Which Has Been Our Delight by janissa11
The Real Reason Dean Owns the Impala by Linda Atkinson
The Demon in Paisley by Linda Atkinson
The Devil You Know by lilmissfury
The House That Jack Built by Nephthys
The House That Treachery Built by Nephthys
The Line by ebolacrisis
The Remains by cherryscott
The Sofa by Linda Atkinson
The Winchester Code by ellipsisblack
There'll Be Peace by zortified
Thin Ice by Morgan
Three ways the Winchesters never lost their memory (2/3) by angstslashhope
Tired and Wired by Shorts
[Alt. link by the Perve Collective
Trespass Series by the Perve Collective
Tumble To The Second Circle by isolde13
Unchained Melody by damerel
Warrior Bond Series by Shorts
Wrong by bloodkisses
AU (Alternate Universe) wherein John and Dean are unrelated or located in a different setting. Feel free to add your fic to the list! In alphabetical order:
Deadly Temptation by angel9in
Betrayal by Shorts
In Humanities Absence by frayen
Living Trapped Inside The Chase by moment_of_sen
The Night Country by destina
The Odds Are by chinas-rose
Unravel by theyscreamofyou