I find most of the Supernatural stories I read through various rec lists, so it's possible that you've seen the same lists and have already found these. But just in case they slipped by you, I present the following:
Like a Rolling Thunder Chasing the Wind and its sequel Mercy Comes With the Morning by elise_509. Contrary to most of what seems to be appearing now, these are Sam/Castiel. "Rolling Thunder" is in 2 parts, and "Mercy" is in 4. I don't read much angel!fic, because I prefer my angels to remain "Other," and so few writers seem to do that in a way that meshes with my imaginings. But these stories are just beautifully written. In "Rolling Thunder," the angels are battling Lilith, and Uriel and Castiel are watching the Winchesters. Castiel comes to believe there is hope for Sam. The angels are never less than "Other." {' He can’t help it. He's known it all along, even back when they were watching the Winchesters from afar. When Sam was still so innocent, unaware of the power he held deep inside, and still clinging to hope of a normal life. He remembers the night that Sam died and how heaven had breathed a collective sigh of relief. Everyone except for him, who inwardly felt a twinge of gratitude when Dean undid what had been done.'}
In "Mercy" Sam and Dean are drifting apart, as Dean is caught more and more in his memories of hell. He's drinking, while Sam hunts alone. Castiel makes the choice to fall from heaven, so he can be with Sam. Sam is still being sought by Lilith, who wants the power Azazel left in his blood. The story is just as much about Dean and Sam rebuilding their brotherly bond as it is about Sam and Castiel. It's wonderful.
And on a lighter note, I offer Sam Winchester and the Prick of Doom by seleneheart. (No, it's not wincest! Although there are a few mocking references to "gay chicken" between them at the end.) It's short -- mostly it's an hysterically funny conversation between Dean and Sam. Dean isn't happy that Sam's sleeping with Ruby. Sam explains: {' “Please tell me you are not actually having sex with that Hell skank.” / Sam shifts uncomfortably, his jeans sliding over the cracked vinyl of the diner booth. “Well, yeah. She’s been the only one around. Plus it negates the whole prick of doom problem.” / Dean nearly sprays his coffee all over his brother. As it is, he takes several minutes of gasping and choking before he can regain his powers of speech. / “Excuse me? Prick of what?” / Feeling more awkward by the moment, Sam explains, “You know . . . every woman I’ve actually, uh, you know, actually penetrated, has died. Ever since Jess.”} And it devolves from there. {' Dean shakes his head. “You’re using holy water to keep demon cooties off your dick?” '}