“It's now very common to hear people say, 'I'm rather offended by that.' As if that gives them certain rights. It's actually nothing more... than a whine. 'I find that offensive.' It has no meaning; it has no purpose; it has no reason to be respected as a phrase. 'I am offended by that.' Well, so fucking what."
― Stephen Fry (on censorship) 

Vice and Wish by thatsakitkat

Vice and Wish - thatsakitkat

An engaging, well written fanfic in which alpha Sam is desperate for omega mate Dean to have his baby. 
N.B. This IS complete despite the AO3 setting.

Source: http://archiveofourown.org/works/1698683

The Doll and the Dummy by homo_pink

The Doll and the Dummy - homo_pink

An excellent short fic in which Jared is a mute mental patient and Jensen the nurse that cares for him. Set in a prison with a block for the criminally insane.

Source: http://archiveofourown.org/works/13176210

Novae Vitae by Sanshal

Novae Vitae - Sanshal

An engaging fanfic in which alpha Jensen accidentally bites Jared, turning him from alpha to omega. This story deals with the aftermath.

Source: http://archiveofourown.org/works/11292123

Dysfunction by Morgan (AO3)

Dysfunction - Morgan (AO3)
An excellent fanfic detailing Dean and Sam's dysfunctional childhood told from Dean's pov.
Source: http://archiveofourown.org/works/667517

You Will Never Claim my Heart by Kleineganz

You Will Never Claim my Heart  - Kleineganz

An entertaining fanfic in which omega Dean is forcibly mated to alpha Castiel. Under his father's influence, Cas attempts to train Dean by force. He eventually realises that gentler methods are needed to woo his omega.

Source: http://archiveofourown.org/works/12044409

Fathers and Heroes by BenLMoore

Fathers and Heroes - BenLMoore
An entertaining fanfic with enough plot twists to cause whiplash. High school quarterback Dean is just shy of sixteen when he first meets 27 year old accountant Sam. The story follows them through the next two turbulent years.
Source: http://archiveofourown.org/works/9566213

More Than We Are by BenLMoore

More Than We Are - BenLMoore

An enjoyable well-written fanfic in which Dean is invited to Sam and Jessica's wedding in California. Weird ass things start to happen as soon as the brothers get together again.

Source: http://archiveofourown.org/works/12682665

Snowbound by KreweOfImp

Snowbound - KreweOfImp

This is a long long fic, I think it got away from the author somewhat. Some nice writing though, KreweOfImp voices Dean beautifully. Cas, Dean and Sam are snowed in the bunker. Cas and Dean attempt to practise their bdsm lifestyle but, to their horror, Sam catches them at play (over and over).

Source: http://archiveofourown.org/works/5706808

The Scent Of You by ImanAngel_YouAss

The Scent Of You - ImanAngel_YouAss

An entertaining angst-filled fanfic from a new author on the scene. Alpha Jensen woos damaged omega Jared when he recognizes his true mate.

Source: http://archiveofourown.org/works/12006192

Splintering in Slow Motion by cyndrarae

Splintering in Slow Motion - cyndrarae

A thought provoking fic in which Jared lives a double life hiding his deep depression following his divorce from Jensen. Resonated with me.

'It’s a common misconception that folks who battle the darkness are easy to spot because of their symptoms. Fact is, many of them are masters at the art of deception.'

Source: http://archiveofourown.org/works/7526416

I Wanna Go Outside (Of Me) by emwebb17

I Wanna Go Outside (Of Me) - emwebb17

A well written enjoyable fanfic in which stripper Dean becomes reclusive Castiel's paid submissive.

“This beautiful, wild, gentle, scarred, hopeful man belongs to me. He deserves better than a broken shadow of a man such as I.”

Source: http://archiveofourown.org/works/5221478

I See the Moon by kaylennz

I See the Moon - kaylennz
A well written curtain/kid fic told from Sam's pov. Sam completes his education at Stanford and wishes to reconnect with his brother. He finds out from his father that Dean suffered a head injury resulting in amnesia and is living a very different life now. (No sex scenes.)
Source: http://archiveofourown.org/works/799092

Take Me Back by Safiyabat

Take Me Back - Safiyabat
An unusual fanfic in which surgeon Dean is cast as the villain and FBI agent Sam the victim. Well written and full of angst, this fic explores the outcome of the incest that began when Sam was eleven. Dean cannot see past Sam's desertion thirteen years ago to understand the circumstances behind his leaving.
Source: http://archiveofourown.org/works/4241112

Please Tell Me Who I Am by Eugara

Please Tell Me Who I Am - Eugara
An interesting ABO fanfic in which beta Sam is turned omega by a cursed object. Sam has to decide which gender suits both his and alpha Dean's needs.
Source: http://archiveofourown.org/works/4795364

Come to Leave Me by raziella

Come to Leave Me - raziella
An excellent new fic by raziella. Present day Sam time-travels back to 1997 and becomes involved with his family prior to all the shit going down.
Source: http://archiveofourown.org/works/7787671

The Road by rivkat

The Road - rivkat
Dean is plagued by the power of psychometry whereby anything he touches promotes memories of its previous owner. Although useful for hunting, the sensation is just too intense for comfort.
Source: http://archiveofourown.org/works/3339119