[moved from my defunct LJ account] A number of these are hosted on LJ, so I don't know if they'll be around much longer,
The Sky verse. I don't think I can even begin to summarize this one. Dean/Castiel, Sam/Gabriel. Hosted on archiveofourown.org.
The Dies Irae series. In this, Dean isn't exactly Michael, no... but Michael's closer than anyone knew. Hosted on livejournal.
The Long Unexpected End. It's the last battle, entirely unexpected, and then... well, Michael and Sammael knew what they were doing, apparently. Which is good, because no one else knew what was going on. Hosted on archiveofourown.org.
And Many Happy Returns of the Day. Beware archangels bearing birthday gifts. This has a sequel, Unwrapping the Gift, which is pretty damn funny by the end. With the apocalypse drawing closer, Mikey might want to get his angelic ass into gear. Both are hosted on fanfiction.net.
The First Born. I'm not even going to attempt to summarise this one. It's good, though, if a little inscrutable. Although, you'll need to go to each chapter from the link here, as the 'next chapter' links didn't work when I tried them. Hosted on dreamwidth.org
Stare Decisis. Uriel and Castiel talk about Sam, and Dean, and their Father's Plan. Hosted on livejournal.
Awake, Arise, Or Be forever Fallen. Kinda similar to Star Decisis. Lucifer and Michael. Sam and Dean. They don't remember who they really are.
Shine. Dean is gone, vanished in a flash of light. Castiel is back, with a handprint to match Dean's and a whispered name on his lips: Michael. And Sam faces losing his brother to an archangel who fell three decades ago… Kinda angsty. Hosted on fanfiction.net.
66 Seals of Doom On The Wall. When Castiel gives Dean 'a weapon to help him in his task,' Dean begins to see that things are more complicated than he thought. Michael is kind of Dean, but also not. Hosted on livejournal.
Fire of Heaven. Dean/Castiel. Five years after her run-in with Azazel, Mary Winchester makes another deal. Hosted on livejournal.
Full Circle. Sam wanted to grab a machete and cut his own head off to stop the headaches. There would be no point in asking Dean to do it he would only say, "No." The selfish bastard. Hosted on fanfiction.net.
It's Gonna Be A Long Walk Home. Dean has always gravitated toward Sam, but neither one of them has ever particularly believed in destiny. Now a demon is after them, their world is falling apart, and the voices in Dean's head might just drive him insane. One thing the boys are sure of: they can't afford to lose each other. Sam/Dean, which I don't like, but some people do. Hosted on dreamwidth.
The Halo verse. This is a good, interesting series, although still in progress. Hosted on fanfiction.net.
Your halo's slippin' down. Suddenly, he wasn't just Dean anymore.
With heaven's help. After Castiel and Dean leave Raphael, Dean returns.
Crowns and thrones. Dean and Sam recieve information on something that Dean is looking for. WIP - abandoned?.
I Got Soul but I'm Not a Soldier. By the same author as the Sky series. Castiel is on the road (saving people, helping things) when he meets Dean and realizes that his soul is different – and not just because he’s the pastor’s son. Absolutely brilliant. Dean/Castiel. Hosted on dreamwidth.
Et In Terra Pax. The end is near. With God missing, most angels being bastards, and the devil closing in on his brother, Dean has to act quickly. Fortunately, Castiel has an idea that might actually give him a chance against the devil. This is one of my favourites, I think. Hosted on fanfiction.net.
With These Broken Wings (Take Flight). The first indication that he is not alone comes when something wraps him in warmth and love. It is the vaguest sort of familiarity. Dean/Gabriel, Gabriel/Michael. Not a pairing I've encountered before in the Dean!Michael trope, but works well. Hosted on LJ.
The Throne. Dean wakes up with a whole new set of memories as Michael the Archangel. When the heck did he say yes? He keeps it a secret. Eventually, Cas finds out. Hosted on LJ.
Of Bastard Saints. Dean is Michael and Sam is Gabriel, but it only gets a mention in the last chapter. Still, thought I'd post it here anyway. Hosted on LJ.
Not In His Shape Celestial. Gabriel works out that Dean is Michael. He has to decide what to do next. This one is actually by me, but people seem to like it, judging by the number of comments. It's complete, but there will be sequels.
Untitled Comment Fic. Dean isn't Michael's vessel, he's Michael. Everyone's favourite Trickster discovers this during Changing Channels. Hosted on LJ.
Account Me Sam. Supernatural/Paradise Lost. Gabriel has accumulated a lot of secrets over the years. He shares some with Castiel. It's written as a monologue, which is an interesting approach. Hosted on LJ.
Reaching As I Fall. Dean/Castiel. Service to God was the meaning of existence; service to Michael is nothing but slavery.” Castiel is part of an underground network helping angels fall, in resistance to heaven. At the same time that a fallen angel by the name of Dean Winchester turns up, some of those in the network are murdered by Michael’s forces – there’s a spy. What does Dean have to do with it? Who is Dean? And why are they hunting him so fiercely? Kinda angsty, but... ends okay. Hosted on LJ.
How Becky Totally saved the World Without Becoming a Mary Sue or: PLEASE R&R OR I'LL NEVER WRITE ANOTHER CHAPTER. Becky/Chuck. The upside of living with a prophet was the fanfic. And the forewarning of the apocalypse. But, mostly the fic. Pure, unadulterated, hilarious crack. Dean doesn't have much of a role, but still. Awesome. Hosted on AO3.
I'm yours 'till they come. During a hunt, Dean lost consciousness near Pontiac. Castiel, a skittish townie librarian, saves him and he offers Dean his house and his hospitality. For weeks they share some kind of blissful domesticity, until Castiel is being made the target of weird angels' "attacks". Unfortunately, this is just the beginning of their problems. Hosted on LJ.
The Sammy and Michael Show. A tale of two brothers on the road in which Sam is Sam, Dean is Michael, it's 2008, and Lucifer is still in the Pit. This is by Lucillia, and is written in their usual light, humorous style. Hosted on fanfiction.net.
Team WHAT?! Sam and Dean are just Vessels, right? Right? This fic is also by Lucillia, and it's absolutely hilarious. Dean and Sam are not, in fact, Vessels, but Michael and Lucifer themselves... but neither plans to admit their real identity for fear of upsetting their current comfortable family dynamic. Meanwhile, no one else has a clue. At first, anyway. Hosted on fanfiction.net. Complete. (Also has a Sam focused side story, Pit Stop in Cambria).
with you and I defying gravity, they'll never bring us down. A short ficlet, worth reading. Hosted on LJ.
Some Dance to Remember, Some Dance to Forget. Short, but interesting, Complete. Hosted on fanfiction.net.
Between the Devil and the Deep Blue Sea. Sequel to 'The Devil's in the Details.' When Sam opened Lucifer’s Cage, the only thing he found inside was Lucifer’s grace – his grace. With the return of his grace, Sam remembered his past – his war against the Host, his Fall, and his plans to bring about the End. The thing is…he doesn’t want the Apocalypse anymore. He likes things the way they are, and tries everything to keep his identity a secret- especially from Dean. Of course, the four Horsemen, Hell and Heaven have other ideas. Hosted on AO3.
Retrospect. They live, they love, they lose, they learn. But still, he is Michael, he is Dean. And they are one. Gen, hosted on LJ.
there, behind the parapets of stone. Coda to 6.06, Castiel knows exactly when the righteous man breaks for the second time. Gen. Hosted on AO3.
Unlikely Places. So the cage opens and Sam discovers that he is actually Lucifer. Now he has to dodge the other angels, the demons, try not to destroy the world and somehow work out how he's going to explain this all to Dean. Turns out it might be easier that he thinks. AU Season 5. Gen. Hosted on fanfiction.net.
I Hear The Voices When I'm Dreaming. After spending thirteen years locked up in a psychiatric hospital for hearing voices, Dean is broken out by a mysterious man in a trench-coat who claims to be an angel. According to Castiel, Dean is Heaven's only chance at saving the Earth from the impending apocalypse - an apocalypse that Dean's younger brother, Sam, is caught right in the middle of. But is everything really as it seems? Dean/Castiel preslash/friendship. Hosted on AO3.
Michael!Dean, Lucifer!Sam Verse. Michael takes the opportunity in the past to have a little chat with the Winchesters, and he has no interest in the apocalypse. Gabriel knows exactly how to stop it. Two fics in this series. Hosted on AO3.
You can also find Dean!Michael fics here and here on spnstoryfinders