Okay, so I'm working on The Laundry List and I'm watching the beginning of Hunted, right? With the confession?
Dean says that John told him he'd have to save Sam, right? And that if he didn't he might have to kill him. I remember when that episode first aired and we were all talking about how it was "so lame" and "so obvious that Kripke switched tracks." How we all thought the big secret was gonna be that Sam was half-YED.
But what if it wasn't? What if that really was the secret all along? What if the "save Sammy" referred to AHBL when Sammy dies?
Think about it, YED even said that Sammy might not have been all him when he came back. And one of the first things Sam did was kill Jake. Sam, who wouldn't kill a possessed/infected kid in Croatoan and who bitched and moaned about Andy being a killer when he shot Webber, shot Jake like, eleven billion times.
The theory relies on John knowing that Sam would die and that Dean would bring him back but that's not really a big stretch. The YED either wanted Sam with him or dead and it;s easy for John to know that. And I don't think there's any way John didn't know what Dean would do if Sam ever died, I mean, hell he was pretty much giving Dean a dry-run on what to do to keep Sam safe.
Given this is a long-shot and likely just the product of it being seven in the morning and me having already been up for about four hours by now, but it's a thought.