I've just read the first chapter of a brand new story called
Sammy in Captivity by
mentholpixie and its amazing and so scary!! Go read it now!
But while I wait impatiently for the next chapter, I'm craving stories similar but a little bit different, something along the lines of this- Sam and Dean aren't brothers or haven't grown up together. One of the boys is taken, by I don't know, a group of creepy scientists or secret experiment captor people, and they're thrown into a cell like situation with the other brother. The other one has been there a while, and is submissive possibly to his captors, he's learned by this point fighting doesn't achieve anything but more pain. Eventually they escape together.
The boys preferably not adults, but I'm not picky and I don't write in blood :)