Okay, so these have been bugging me for a while now.
First, I read a Supernatural/Sentinel fic that was set somewhere in Season 4. May or may not have been set after Dean regained his memories of hell. Anyway, Dean awakens as a Sentinel, with Sam as his Guide. It's mostly from Jim's POV, I think, might be some time after the end of Sentinel. Sam got Blair's help by sending a picture to his phone? Something. Anyway, Jim was looking for them and before he found them he saw Sam and Dean's spirit animals. Dean's was a griphon, while Sam's was a dragon. I remember Dean said something about it later, and Sam wanted to know the color of his dragon spirit animal, to look it up or whatever. There was also a second fic, seperate I think, where Jim dreams of the blue jungle, but he goes to the edge and sees a desolate landscape. Dean's griffin is there, chained down and being attacked by something, and Jim helps break one of the chains so the griffin can fight back.
Lot of detail, I know, but without a title or author, I've been SOL.
Second, I don't have as much for. I think it was a crossover with either Criminal Minds or Bones, but I'm not sure. The only thing I really remember is this scene where Sam is in a jail cell, and they're trying to get him to flip on Dean. Sam showed them the scar where Jake stabbed him and tells them that if it weren't for Dean, he'd be dead. Somebody (Reid? I don't know.) said that from the looks of the scar, he should have been either dead or paralyzed.
Third is much more light-hearted. It was taking lines from the episodes and expanding them to be as cracky and wincesty as possible. There was something like a season per chapter and it pulled no stops on the perverted train. I remember in the "improved" lines from Devil's Trap, Dean said something about how he knew that wasn't their father because he hadn't put his hand down Dean's pants. The demon pretty much got disgusted, saying how he thought that was just a weird fantasy, and left.
Edit: Yay! All found!