Aha! You know, I hadn't even thought of that when I watched "Bloody Mary." But you (and other fans) are right in wondering why his eyes bled too. I do think that they had to be referring to a specific secret, from the way the report talked about it -- they were confirming that we'd find out about a particular secret, as opposed to just saying Dean had a secret we'd hear about. Oh, the possibilities!

As for SG: the first thing that comes to mind is from "Ripple Effect." Joe Mallozzi described some deleted scenes from the episode, one of which was intended to imply that Black!Daniel and Black!Cameron were in a relationship. Black!Daniel was being interrogated by our Cameron, and was "testing" him by hinting about the Hunan House -- supposedly Cameron's favorite place for ginger beef, and the first place Cameron did something significant (we don't know what).

(Another deleted scene had B!Daniel and B!Cameron arguing on the Prometheus because B!Daniel was upset about what they were doing; it read as being really intense, and after B!Daniel walked away, B!Cameron was so upset that he tried to put his fist through a wall, if I remember correctly. Again it implied deeper feelings ^_~)

If that's not what you're thinking of, I'll scrounge around in my brain for what else it could be!