The first one was very old at least 2009, I think it was never finished... not sure.

1) It was Jared/Jensen, Jensen was sold by his family to a man who kept him guarded all the time, and the first scene is the guy having sex with him, and forcing him to keep his eyes open.

Then a team of SWAT like guys kidnap him to punish his owner. Jensen is severly traumatized and can't act normal with other people, fearing his owner would get mad.
Chris and Jared are part of the team that rescues/kidnaps him, Chris becomes Jensen's friend and protects him, until he's almost normal, and even chats with others. but Jared wants to seduce Jensen for kicks

At some point Chris is sent away and Jared is the only one left with Jensen


2) I'm looking for  is a fic like a year or two ago too, Jared is some kind of black ops agent and he's banging Chad - I think-.
he's asigned with Chris to a mission and he's given a clon/enhaced partner for it, it kinda foillows the logic of Dark angel.

Jared is given Jensen but then I lost it, Jeffrey was there too, as the CO.
Someone? please?

(If I made any mistake I'm sorry)