Let me start by saying that some of these I read quite awhile ago, so my memory on the details of their relationship may be spotty. That being said, here's a handful of my favorite polyamory fics that I think fit your requirements:

Like Luggage of Some Departed Traveller (http://britomart-is.livejournal.com/180851.html) by britomart_is: "Rogue wildlife attacks? Check. Virulent, incurable pandemic? Double check. Relentless string of natural disasters? Check, check, check. Dean's got it hard enough dealing with the collapse of modern society, so imagine his dismay when he goes to Stanford Law to fetch the brother he's been painfully in love with for most of his life and finds that brother happily married. When Sam, Dean, and Jess set off across the country to find their dad, it's all they can do just to stay alive, much less stay true to each other." (Sam/Dean/Jess; post-apocalyptic)

Imagine the Houses (http://elohvee.livejournal.com/397032.html) by elohvee: "Golden Gate goes down on a Tuesday. Middle of morning rush hour, salt-fog and winter rising up off the water. Some tourist sells CNN his footage from Fort Baker for ten grand, and for hours it's all that's on, over and over: just the same shaky film that shows the beams snapping like twigs, the cables plucked out like puppet strings. Cars spill into the bay. Someone screams in the background, a long, unbroken note that rings in Sam's ears even when the camera cuts back to the solemn-faced anchor, talking about tragedy and alleged terrorism." (Sam/Dean/Jess; post-apocalyptic)

And the Devil Makes Three (http://archiveofourown.org/series/9262) by killabeez: "Dean never thought he'd be the one living the apple pie life. There's a lot of things he never thought would happen." (Sam/Dean/OFC; post-series AU)

Fade to Black (http://runedgirl.livejournal.com/45473.html) and Black is the Color of My True Love's Eyes (http://runedgirl.livejournal.com/48284.html) by runedgirl: "The brother that Sam gets back isn’t the same, but Sam’s love is. Sam risks everything and leaves everyone he’s ever cared about behind in the desperate hope that the bond between him and Dean might just be strong enough to transcend what hell did to his brother. Set post Season 3, seven months after Dean’s deal came due and written over the summer before it was AU, this story just kept writing itself and wouldn’t let go until it was an epic love story in every sense, eventually spanning five decades with enough twists and turns to make me dizzy." (Sam/Dean/Ruby; post-series AU with demon!Dean; heed the warnings)

Brothers Called Bini (http://infatuated-ink.livejournal.com/40997.html) by infatuated_ink: "When Sam went to Stanford, he left behind a twin sister and an older brother—he’d been sleeping with both. Now, Dean and Jess come back into Sam’s life and Sam sees the effect leaving had on all three of them." (Sam/Dean/Jess; sad; Jess is Sam's twin sister)