Okay, the episodes are pretty much all excellent from Seasons 1 and 2, this episode was well executed. Jensen and Jared are exceptional actors and are always surrounded by wonderful counterparts, whether a guest appearance or a regular.
"My take; Sam and Dean's Mother is some sort of part supernatural being and was kind of hiding out from whatever past she had. The yellow-eyed demon finally found her and corrupted Sam because he was an infant, Jared was older and more self aware. In the final episode Jared will somehow trap the demon and be forced to make a deal where the demon will bring Sam back and Dean will let the demon go."
Or, Sam's real father is the yellow-eyed demon, which would make for a really bad cliché. I have faith in the writers that they will not make this show just another cliché.
Peace,
Slackwoo