Forewarning, my preference is BLINDINGLY obvious with this list. That preference being: the Winchester boys’ needy, desperate, all-encompassing codependency. So, therefore… All of these fics have a LOT OF FEELINGS, and they will make you FEEL THEM ALL. 

• Last Outpost of All There Is - Dean/Sam - this is my favorite fic of all time. A different kind of apocalypse plays on the boys’ overwhelming codependency and UGH SO MANY FEELINGS I CAN’T gkadjgh Everyone and their mom should read it
• The Howl!Verse - Dean/Sam/Dean - askljfahsf THIS IS THREATENING TO TAKE THE FAVORITE SPOT, TBH. Omg it’s everything I never knew I wanted. Sam saves Dean from Hell and they both come back… different. It’s a lot darker than these other fics, but in a perfect way. If you can’t handle blood, don’t read it, but omg it’s soooo delicious and perfect
• Freak Camp: A Monster By Any Other Name - This is a monster of a fic itself, very long and very rich and it hurts soooooo muuuuuuch. It’s depressing and painful and beautiful and ugh. AU plotline where Sam grows up in this like concentration camp for monsters and little baby hunter Dean takes a liking to him and visits him a lot and UGH FEELINGS
• Dark Side of the Moon - Sam/Dean - I think this was my first wincest fic I ever read, and THANK GOD it was this, because it set the bar. Dean has a curse that blinds him and makes him deaf and it’s so needy and codependent and naughty and delicious and FILLED WITH FEELINGS
• A Bleak Understand in Reverse - Sam/Dean - Sammy slowly dying from a brain tumor, because, you know, wincest shippers are all masochists and we want to CRY OUR EYES OUT
• Treasure - Sam/Dean - this story is beautiful. Post apoc story with zombie mutant things and the Winchesters part of this survival group similar to The End. I read this completely enraptured. 
• A List of Typos Made by God - Sam/Dean - amnesiac Dean. But it’s a weird kind, he is only forgetting Sam and everything about Sam. Pain. Maaaan, all I can say is painful. And yet beautiful.
• No Line on the Horizon - dying Dean. Because you haven’t cried enough. This is an alternative to the entire show, Dean shows up at Stanford like in the pilot, but because he’s dying and wants to be with Sammy, instead of hunting and looking for dad. FEEELINGS AND TEARS
• The Year of Letting Go - Sam/Dean - Dean goes deaf and blind and HOLY GOD THE FEELINGS. I keep saying that. XD BUT REALLY. This is beautiful. That intense codependency thing again that is just overwhelming and akjhgagljk
• We Were Twenty - Sam/Dean - FLUFFFFFF, it’s so warm and fluffy and then sad and ugh. The boys retire after Sam gets hurt too badly to keep on hunting. They settle down together and the entire fic should be read while you hover over hot chocolate or something
• The Land of the Blind - the world as they know it is over and Sam doesn’t remember. Broken Sam for all the feels
• Words for Snow - another apocalypse story and Sam can’t talk anymore. This one for all the HAPPY WARM FUZZY FEELS.

UPDATE:

• Closing Time and the sequel The Last Year At Harvelle’s - Beautiful perfection soul-crushing post-series fic that somehow both makes me super happy and make me want to die. Actually, you know what? Just go read EVERYTHING Amanda writes. She gets into Sam and Dean’s minds like no one else and her writing is seriously perfection. 
• Wolfpack!Verse - Dean/Sam - Ugh this is just FANTASTIC. An AU retelling where the boys and John aren’t the good wholesome hunters we know. The name of the fic really fits perfectly, because that’s what they are in this, a pair of wild wolves who stick crazy close to the pack.
• If They Send The Wolves, I’ll Join The Wolves - Dean/Sam - Ow. My. Everything. Sam’s in hell, and Dean finds a way to see him for one night once a month and it is so ajfjgfjfhsg
• A Thousand Shades of Red - Dean/Sam/Dean - Some pre-series pain for your reading torture I mean pleasure
• The Truncated Love Story of Smith and Wesson - ~*~*~swesson~*~*~ Smith and Wesson head out on the road and get themselves their first real hunt and it’s actually super really adorable until LOLOL HERE ARE YOUR MEMORIES BACK. but then it goes back to adorable
• Consequentiality - Sam/Dean - when Sam’s wall breaks, Dean literally binds his soul to Sam’s to keep his from shattering, and now their codependency thing is a whole new level of intense and akjgdhgjkadhgkjadghakdjhdkgjadhgjk dfgadh
• The Theory of Relativity - Dean/Sam Sam/Jess - omg this is a fluffy cute post-apoc for once. They’ve won and they’re settling down because Sam starts writing and becomes this famous author and it’s just super cute domestic cuteness
• Stranger Than Fiction - Dean/Sam - OMG LOOK GUYS! A HAPPY FUNNY TOUCHING FEEL GOOD WINCEST FIC! On my rec list wtf!? Anyways, the boys + wincest fanfiction = hilarity, brother feels, smut, and more hilarity 
• Gone Again - Dean/Sam - …… I see nothing but pain here. Sam and Dean both really really really fucking want and need and want each other but everything is too fucked up and omg it’s just heartbreaking. It also has a prequel - Gone, and a sequel - Never Mind That that were written afterwards