I had to mull this question over because I have read many pieces of fanfiction, mostly all Dean/Castiel (because that's how I roll), and many of them that I found enjoyable and well-written enough to save and place in my memories. To consider something a favorite means the ones I have been deeply affected by. There's definitely a lot I could rec out to everyone, but that would take forever. So here are my top favorites as of right now (in no particular order):
01. The Voice of the Turtledove by obstinatrix
Castiel was eleven years old when he first felt there was something wrong with him. He's twenty-nine, a Roman Catholic priest in a small New England village, before Dean Winchester shows him that there isn't. AU.
I honestly don't think there's been a piece of fanfiction that has affected me more than this one. I consider it more of a story than your average fanfiction, since it flows so well with the raw emotion and characterizations and growth and, you feel emotionally attached to the characters and the situation unfolding. This one is, by far, one of my top favorites within the entire fandom. ♥
02. The One Where Dean Meets His Adviser by moorishflower
College is hell. Between classes, his annoying little brother, and his inconvenient (and possibly not exactly legal) crush on his advisor, Dean Winchester is learning that firsthand.
This is the first chapter of the Cold Academic Hell 'Verse that the author is still currently writing, so it's a WIP, but it's an amazing work-in-progress just the way it's written. I can't really explain it, but reading these makes me have these warm fuzzies because it's too cute. The 'verse shares the Side B portion including Sam/Gabriel, but they are separate stories so if you're not into Sam/Gabriel you can only read the Dean/Castiel Side As. ^_^
03. A Rain of Feathers by laceymcbain
Sex pollen Angel!Porn with a plot. No, seriously.
Just as the summary says, this is perhaps my first step into the sex pollen trope which is my favorite form of kinks ever. But while I love my PWP sex pollen fics, this one is a mixture of Porn With Plot that interweaves itself nicely, from the storytelling to the characterizations, this is incredibly well-done. I blame this for being the start of my sex pollen kink addiction, just saying.
04. The One In Which Castiel Doesn't Fall by tracy
This is how Castiel's love story goes.
This is heartbreaking and beautiful all at the same time, just really exploring Castiel's love for Dean and his understanding of his love and feelings for Dean. Words cannot convey how much I adore this fic.
05. Immortality Meant Never Dying by tracy
He had come alone and knew not what he had come for, a vague mission from a far vaguer father, seek in the shadows and the pits for something, someone, who holds the fates of angels and men in his bloodstained, broken, bleeding hands. See if there is anything left to salvage, and if there is, bring him forth to serve the Lord and his Armies against the Darkness.
This? Such perfection of describing how Castiel rescued Dean from Hell. I've read various scenarios, all unique and different in how it was done, but this is perfectly laid out to how Castiel reacts to Dean's soul, how he protects and cherishes it, and it's so amazingly well-done that you'll end up loving it too, if you haven't read it already. Definitely one of my favorites of Tracy's works.
06. Words and Hands by entangled_now
"You'll need to take your protection seriously from now on," Castiel's voice sounds even deeper than usual. Bathroom acoustics suit him. He should make speeches about how they were all doomed in here more often.
I love this one because of the unresolved tension between them, like always, but there's a sereneness and safety connected in just a mere moment of Castiel teaching Dean how to protect himself from other angels via written sigils. I love how it's written, and it makes me wish something like this really happened on the show because it's subtle enough to not be definite but strong enough for that kind of subtext between these two.
07. 300 Things by cautionzombies
Dean's life at twenty-four makes him feel like he's forty--he works two jobs to help pay bills for his house and put his genius little brother through private school, and has spent six years (on and off, let's be honest) working on his mechanical engineering degree at KU. With so much of his life devoted to his family, Dean has little time in his schedule for class and no time for social interaction. Then, while getting his classes together for the fall, he finds himself in a do-or-die situation: He must take his last literature class now, his spring already filled with those left for his major...except that none of the English classes will fit his schedule.
This is how Dean grovels and begs Dr. Castiel Milton to make a special arrangement for him, and Dr. Milton does.
I'll let the summary speak for itself. Once not being able to read AUs, I've grown to love them, as seen from the other recs I've provided, and this one is no expection. It plays on my professor!Castiel kink (like, massively) and while still a WIP, this is also another amazing story woven together to engage you with what is being unraveled with the characters and their situation.
08. Chrysler Almighty by zatnikatel
He stops, and Castiel hasn’t moved, and his expression hasn’t shifted, he’s still just staring back at Dean, and his eyes are blank and unreadable. When he finally speaks, his tone is ill-tempered and acidic enough to set alarm bells ringing in the small part of Dean’s brain that’s still sober enough for rational thought.
An absolute and undeniably smoldering hot wall!slamming angry!sex fic, which goes through the motions of what has been happening this season and will get people who are confused and unhappy about how Dean has been treating Castiel in S6 to have it be resolved by unleashing their unresolved sexual tension in the one way they know how, of course. Includes bamf!Castiel taking control, another turn on for me.
09. The Man Who Would Be King by leighleighla and irnan
After killing ALL of the more powerful demons in the underworld, Dean is now pretty much in charge, especially after he challenged Lucifer to a game of quarters for his throne.
THIS IS A GEN STORY, PRE-S4! SHOCKER! Seriously, when I discovered this fic randomly I was laughing so hard. It's the most ridiculous cracky genfics I've read for this fandom.
Rest of the 30 Days of Supernatural Challenge.
Nearly everything is going on hiatus right now, I almost forgot that there was a new episode tonight, lol. Although I'm fearing the worst for a particular minor character that we've all grown to love and appreciate. ;__; WHY MUST YOU BE SO PREDICTABLE IN FATING YOUR CHARACTERS SHOW, WHYYYYY?