Okay, so the first story I can't find is one where Sam wants to give Dean a child, so he asks Cas for help. Dean gets the wrong idea and thinks something's going on between them, but when Sam explains Dean pretty much jumps poor Sam, heh.

The second fic I'm *pretty* sure is J2. They're both part of this.. government run thing that they don't have a choice about being in. All who are in it become an Alpha, Beta or Omega, and their training differs depending on what they are. Jensen leads student Jared's group onto a new planet, I think? Anyway, it's just the two of them when they figure out that Jared's an omega and something in the area is setting off his heat. And the usual happens. I remember there being a sequel where they were split up and Jensen gets really aggressive and violent, while poor Jared's just about going crazy from lack of sex.

Help will be much appreciated, since obviously my Google-fu sucks. XP

FOUND - Both fics have links in the comments.