2a - This one, I believe it was in which John is an alcoholic and abuses the boys. But Dean always tried to keep it from happening from Sam and taking the beatings on himself. They eventually leave their father, and move far away from him. When he's older-Sam starts to have visions which lead them to the hunt, and at the end John finds them and ends up shooting and almost killing Sam. It's been a while since I read it, but that's pretty much what I remember of the story.

2b - In which Sam had a girl-friend who was abused as well. It was a WIP and I don't remember much anything else.