A Thin Chain of Next Moments, by batyatoon and dotfic. Het, Sam/Ava, Dean/OFC, John. (ca. 22,000 words)
In this AU Dean makes a deal with the Crossroads Demon to free John from hell, and gets the standard ten years contract. On the one hand this AU is quite sad, on the other we get to see Dean live for a decade. (Also on AO3.)

But Deadly series, by Bella Temple. Gen and het, Sam Winchester, Dean Winchester, Bobby Singer, some Sam/Jess. (ca. 38,00 words)
I find the setup of this AU really intriguing. Here John was killed by the YED, Sam and Dean grow up with adoptive parents because Mary left their home right before the demon attacked for a reason initially hinted in the series, and other stuff going on too... anyway, the series had me hooked.

Steam, by Bella Temple. Gen, Sam Winchester, Dean Winchester, some Dean/Steampunk!Impala bonding. (ca. 30,000 words)
In a post-apocalyptic world Sam and Dean try to figure out what happened, to find other survivors and to make the impala run on steampower. I enjoyed the mystery and the plot twists here, and of course a Steampunk!Impala with Dean as its engineer is awesome.

Art Therapy, by CaffieneKitty. Gen, Dean. (ca. 1,200 words)
In this AU Dean was the only survivor of the fire. What gives this story a great twist is that it is written from various outsider POVs of report cards and therapy notes. (also on AO3)

Five Things that never happened to Dean Winchester, by Cccarioca. Slash and het, Dean/OMC, Dean/Bright (from Everwood), Dean/Jess, Dean/Sam. (ca. 7,300 words)
I liked all the scenarios, though especially the role-reversal one (what if Dean had left for college?), and the rather bleak look at Dean and Jess had Sam been killed instead of her, besides the Everwood crossover has Zombie!Colin, which is just awesome. Unfortunately the journal has been deleted, but the story can still be found via the Wayback Machine at the link above.

Five Families John Winchester Never Had, by Cofax. Gen, John Winchester. (ca. 4,500 words)
In this "five things" story I especially liked the last one, a "Mary survived" AU, but the others had interesting premises as well.

Rising Storm, by Cofax and Hossgal. Gen. (ca. 11,000 words)
This is a fusion with the Finisterre universe. I haven't read those books, but they made for a cool AU scenario of settlers on a hostile planet with telepathic fauna.

Untitled SPN Snippet, by Cofax. Gen. (ca. 1,300 words)
I wanted this to be longer and an apocafic epic rather than a snippet, but the world building was still interesting.

And Won The Soul's Rest, by Concernedlily. Gen, Sam Winchester, Dean Winchester. (ca. 31,000 words)
This is a medieval AU with Sam as a monk and Dean as a mercenary, and the plot parallels to canon with the demon worked very well. As a Big Bang story it also came with art by Glockgal and Reallycorking that complemented the story nicely. (also on AO3)

Family Values, by DevotedFan. Gen, Sam, Dean, John. (ca. 3,800 words)
What if the demon had taken Sam that night to raise him?

Scheduled for Termination, by Dolimir. Gen, Mary, Dean, Sam. (ca. 20,855 words) This is a fusion between Supernatural and the Terminator universe. Here Mary survived the demon to become a hunter, which in turn equipped Dean to become part of the resistance. Then of course there's the Terminator kind of time travel, so in the end poor Mary has demons after her one son and robots after the other.

Dromoscope, by Emily Brunson. Gen, Dean Winchester. WIP
It's a fusion with the novel "Jumper". I haven't read that, but still enjoyed the story so far. The premise is that Dean is able to teleport, and keeps this secret from his family.

Family Secrets, by Ignipes. Het, Sam/Jess, John/Mary. (ca. 1,200 words)
How the Winchesters might have been had both Mary and Jess lived, but the Supernatural was still out there.

Physiologus, by imogen. Gen, Sam, Dean. (ca. 5,630 words) In this AU Sam was pre-med instead of pre-law and tries to find a scientific order in the supernatural phenomena they encounter.

Appointed Verse, by Irnan. Het, John/Mary. WIP
A Mary-centric AU verse. Mary survives, and she and John become hunters together.

Pathways Verse, by Irnan. Het, John/Mary. (ca. 36,000 words)
This is another Mary-centric AU verse (though Sam and Dean appear too), that gives her an interesting supernatural background of reincarnation and connects her to Samuel Colt as well as Ruby.

Teufelshunde, by July. Gen. WIP
In this AU Sam and Dean grow up with a foster parent after John has been arrested. I really like the OC and the structure with the flashbacks here works for me, even though flashbacks aren't my favorite things.

The Boy Who Walked On Stilts (part 2), by Kellifer_fic. Gen, Dean Winchester, Sam Winchester, Bobby Singer, Pastor Jim. (ca. 6,640 words)
The premise of this is that John died early, and Sam and Dean are raised separately by Bobby and Pastor Jim for reasons that become clear over the course of the story.

A Heartbeat At My Feet, by Kellifer_fic. Gen, Dean Winchester, Sam Winchester, John, Winchester, Bobby Singer. (ca.7,400 words)
This is a fusion of Supernatural with His Dark Materials, i.e. Sam and Dean have dæmons.

Older Than The Days He Had Seen, by Kellifer_fic. Gen, Dean Winchester. (ca. 3,700 words)
This AU is rather sad. It explores how the Winchester family would have been different and yet the same if Sam and Dean had had an older brother.

The Crow on the Cradle, by Kroki_refur. Gen, some Sam/Jess. (ca. 98,200 words)
The starting point here is that one day Sam walks out on Jess, who then searches for him together with John and Dean, and learns about hunting. Not just has this story Jess as a hunter, but Sam is kind of broken in an interesting way that I don't want to spoil too much. Unfortunately the LJ version has been locked but the story is still available for download at the Ebook Library I linked here.

Berserker!verse, by Leonidaslion. Gen, Dean Winchester, John Winchester, Sam Winchester, Bobby Singer, also some het, Dean/Cassie.
During Sam's Stanford days Dean has an unfortunate encounter with a berserker (in the context of this universe someone sharing their body with an animal spirit which more or less grants various superpowers), which leads to a wolf spirit choosing Dean as a host. Much angst and complications follow. The series eventually progresses through the first season episodes. There is also a rather epic slash continuation of this universe, Fetters of Fenrir (mostly Sam/Dean, ca. 200,000 words), and even though I'm not much into Sam/Dean as a pairing the universe interested me enough to want to read all stories in it. And I enjoyed that novel for the plot which had me hooked, for Dean being hurt in various ways, and also for the supernatural mythology bits about the demons and the berserkers here, even though incest soulbonds are not one of my kinks.

And Everything Nice, by Lyra Wing. Gen, Sam, Dean, OC. (ca. 6,550 words)
I didn't really expect to enjoy an AU in which Sam and Dean have a sister who grows up with them, but gave it a try because I usually trust this author to be entertaining, and this AU really pulled me in, was a great read and I liked the original character.

The Sunless Land by Lyra Wing. Slash, Sam/Dean, Meg, John. (ca. 11,700 words)
It's kind of rare for me to read Wincest fic, but that they didn't grow up together in this AU made it much easier for me to buy that they'd be attracted to each other, and I have a soft spot for stories in which Sam is kidnapped by the YED and grows up with him and Meg, especially when they are not OTT dark fic, but the demon is still creepy, like in this one.

To Catch a Thief, by Lyra Wing. Gen, Sam Winchester, Dean Winchester. (ca. 8,600 words)
A while back Lyra Wing wrote an AU with Sam and Dean as FBI agents (Paradigm Shift, this is the prequel giving the background how they ended up that way. It splits from canon before the season two finale.

Fistful of Rain, by Marina Rusalka. Gen. (ca. 9,450 words)
This is a "five things that never happened" fic, focusing on Dean, and all the scenarios are very plausible.

Revelations, by Marina Rusalka. Gen, Victor Hendricksen, Dean Winchester, Sam Winchester. (ca. 24,200 words)
Here, Dean is an ATF agent who works with Victor Hendricksen on the serial arson case of the demonkids' ceiling fires. I enjoyed that we were led into this AU through Hendricksen's POV, and how Dean and Sam's backstory was revealed gradually. Also it has great art by Ileliberte.

This Wheel's On Fire, by Marina Rusalka. Gen, Dean, Bobby, Sam, Jess. (ca. 27,800 words)
This is a fusion with the movie Ghostrider. I haven't watched that, and don't think familiarity is necessary as the basic explanations of the Ghostrider premise were covered and merged with SPN mythology too. In any case the image of the flaming Impala leaving blazing tire tracks is better than a flaming motorcycle, and I loved Dean's conflicted reaction to being a Ghostrider.

Game of Life, by Mary. Gen, though Sam/Jess is implied.
It's five glimpses of other possible lives with a focus on Jess. (Sadly, I don't have a working link to the story anymore.)

Gingerbread, by Mary. Gen.
This is a plausible and deliciously creepy AU in which the demon pushed his agenda harder and kept closer taps on its victims. What if the demon had possessed John the night of Mary's death? (Sadly, I don't have a working link to the story anymore.)

Grounding, by Mary. Gen, Dean. (ca. 960 words)
Short snapshots from an AU scenario in which John left Sam and Dean with Ellen and Bill. (Sadly, I don't have a working link to the story anymore.)

Rain Falling Down, by Maychorian. Gen, Bobby, Castiel, Jimmy, Dean, John. WIP (the series, individual stories are finished, ca. 20,000 words so far)
In this AU Castiel travels back in time to prevent the apocalyse, but things go wrong and he gets stuck in his host as a kid without his full powers, and lots of angst and h/c ensue.

House of Burden, by Maygin. Gen. (ca. 76,600 words)
In this AU the fire never happened, and only Sam finds out about the supernatural because of his visions.

Light of Day, Dark of Moon, by Maygra. Gen, Dean, Sam. (ca. 3,135 words)
Sam and Dean are under a curse like in the movie Ladyhawke.

My Life's Come Off Its Tracks, by mimblexwimble. Gen. (ca. 28,700 words)
In this AU Dean gets sick as a child, forcing the Winchesters to adjust. We see events from through Sam's eyes and I find good children's POVs really rare, but this one worked for me.

Gimme Shelter (ca. 7,940 words) and its sequels Paint It Black (ca. 1,330 words) and Rain Fall Down (ca. 2,185 words), by Nilchance. Gen, Sam, Dean, John, Bobby, Missouri. The individual stories are finished, but the universe is still a WIP.
This is a rather bleak AU scenario that explores what might have happened had Mike Gunther called Child Protective Services.

Cold Ashes, by Pix. Het, Sam/Jessica, Dean. (ca. 3,700 words)
This explores what might have happened Had Sam refuse to leave Stanford with Dean. It's been written when we knew even less about the demon, so I'm not sure it could have turned out like that, but I still liked the story.

Daylight Refracted, by Pix. Het, Sam/Jess, Dean. (ca. 7,585 words)
This is a really happy making AU in which Jess comes from a family of hunters, survives the YED's attack, and hunts together with Sam and Dean.

Golden Lights Go Dark Tonight, by Pix. Gen, Sam Winchester, Ruby, Dean Winchester. (ca. 5,100 words)
I guess this AU is a take on the old theme of the road to hell being paved with good intentions. DarkSide!Sam is not normally my thing, but this story puts an awesome twist on this. It's a dark AU that sucker punches you with its brilliant premise.

Cover Your Plans In Sand, by Port. Gen, Sam, Dean, John. (ca. 3,500 words)
In this AU Sam died in a mundane way six months before Dean came to contact him at Stanford. The story is mostly about Dean's reaction, but there's flashbacks in which Dean reminisces too. (also on AO3)

When the Badger Grows Horns, by San Antonio Rose. Gen. (ca. 25,800 words)
The premise of this AU is "what if John Winchester was Diné?" and what made this most interesting for me was to see Sam and Dean with more extended family to fall back on and fewer rifts between them.

Miles Before I Sleep, by Silverkit. Gen, Sam Winchester (there's a brief Sam/OFC sex scene but no relationship). (ca. 1,860 words)
It's a great, if painful, look at a Sam who decided not to go to Stanford, but to stay with his family.

The Heist, by Starrylizard. Gen.
This isn't a fic rec, but an AU vid. It is really fun though. Sam and Dean are bankrobbers.

And Burn the Long-liv'd Phoenix in her Blood, by Tabaqui. Gen. (ca. 6,800 words)
In this AU Mary survives, but they still hunt. I enjoyed the setup and look at their lives.

Clay And Paste And Down, by Troll Princess. Het, Sam/Jess, John/Mary. (ca. 3,500 words)
It's wingfic, but handles it in a somewhat unusual way, i.e. in this AU Dean was born with wings.

No, Make Something Up, by Troll Princess. Het, Sam/Jess. (ca. 3,750 words)
What if Sam had come clear with Jessica about his family while he was at Stanford?

Straight On 'Til Morning, by Troll Princess. Het, John/Mary. (ca. 3,860 words)
In this AU Mary survived the demon and the fire. The Winchesters are still hunting though.

They Say It's Wonderful, by Troll Princess. Gen. (ca. 7,400 words)
That night the demon did more than just killing Mary, and as a result Sam didn't grow up with his father and brother. (Being any more specific about the premise would spoil things.)

Show me a hero and I'll show you a tragedy, by Unperfectwolf. Gen, Dean Winchester. (ca. 2,575 words)
The premise here is the basic "what if Sam and Dean grew up 'normal'?" that is they haven't been raised by John but by other relatives, though John is alive. What it made it stand out to me was that the reality of the demon and John's hunting of supernatural monsters remains ambiguous throughout.

Clangs, by Vehemently. Gen, Sam Winchester, Dean Winchester. (ca. 14,800 words)
This was a rather creepy and bleak AU. At first I was confused about what exactly was the premise leading into this (which I won't spoil for you), but then when it became clear, it was even more horrible and hopeless than I expected. But it's a really effective, though tragic, "what if" scenario. (Also on AO3.)

Not in My House, by witchofthedogs. Het, Sam/Jess.
The demon doesn't attack Jess until after Sam finished law school, they married and their son is six months old.