I was waiting for the reruns before posting these.
First, we have a not-so-secret secret from the Yellow-Eyed Demon, probably Jossed by the finale.
They have Dean in the place where it's hidden. Next, we have a secret from Dean from Tall Tales.
Computer was fine. User is horny. Last, we have two from Sam from Heart.
I know we're all thinking it. I'm just saying it. Safe Sex and the Single Werewolf