Hence, some John/Dean recs! Though you know, if you're looking for smut or John and Dean picking out curtains, then these are not the recs for you. Because...
Caveats: Although I love Sam/Dean (and some other brothercest fandoms pairings) like breathing, I have serious trouble with parent/child incest. I don't think that situation can ever be truly consensual because of the power dynamics inherent in the relationship. Or if it IS consensual... then both parties are seriously f***ed up.
As a result, I tend to go for the angsty John/Dean stories. Here below is a collection of marvelous and intriguing AU John/Dean stories-- and I do mean AU, some of them more obviously so (because they're based on scenes we know but have taken off in a direction that didn't happen in canon, or because certain people or no longer living or what-have-you). The others are AU to me, because although I really don't consider John Winchester a good father (sorry, John fans!), I also don't believe the reality of John could ever bring him to have sex with his children.
Night Country (NC-17) by destina. For the two people who haven't already read this, it's post-S1 "Devil's Trap" and is Demon!John/Dean. Do you remember that scene in the cabin where Demon!John was all up in Dean's space and the air was crackling with dirtyBadWrong sexual tension? I know I do-- I think I even begged Smidgy to make icons of it. This story begins in that scene, and continues forward out of canon. This is an angst-fest, with Dean searching for healing after being raped by Demon!John, and with the boys being afraid of John (and what he might carry within him) and ultimately John being afraid of himself. Great development of the central dramatic theme, features Bobby and excellent Sam and Dean. I wish there were a little more classic H/C in this story, in the relationship between Sam and Dean, but that's mainly because Dean's being kind of an ass about it. And I can't say that's at all unlike him, unfortunately.
Honor Your Father (R) by feline_fury1. The summary is, "Sam's been dead 15 years, and Dean makes himself pay for it each and every day." Definitely AU, dark and angsty and yet there are hints of light in the most unexpected places. This is a fascinating read, and not so devastating that it will destroy you. Highly recommended, for the intriguing Dean POV.
The Lesser of Two Evils (R) by cria_ecrit. John/Dean, Sam/Dean, this one is fully of angsty mixed emotions and pathos, and the style is lyrical and haunting.
And The Moon Hits The Water (R) by kissedblister. This is really a John/Sam fic, with unrequited Dean/Sam, John/Dean. It's wrong, it aches, and the language and emotion are incredible. Seriously AU, very quiet tone, and what a punch it packs.
Familiar Admonishments (NC-17) by teand. I recc'd this before, but I can't leave it out in a post on John/Dean recs. It's dark, it's full of ache, the Dean POV is incredibly well-written, and the relationship between him and John is full of wrongness and in some ways is just so inevitable. One of the darkest and best stories I've read in this fandom.