I once read a John/Dean story, and I can't remember the name of the author, but I believe the story was called Feral. John is bitten and turned into a feral, and leaves Dean before feral instincts overwhelm him and he takes Dean as his mate. Sam is at Stanford, and Dean doesn't want to be alone, so he goes to the pack and asks to be turned as well, and voluntarily becomes John's mate. The story's main focus is John's pack stopping another pack of "bad guy" ferals who are turning humans against their will. Near the end, both Sam and Jessica join the story as well.

All I can remember about the John/Ellen story is John is brought back from the dead to help the boys break Dean's crossroads deal, and he does it by helping Sam remember some crucial detail from their childhood. While trying to find his sons, John and Ellen don't exactly fall in love, but they do acknowledge and act on their mutual affection/attraction. There was also an OMC, an African-American named David who turns out to be immortal. Bobby was also in the story -- he's the one who reveals David's supernatural, because he saw the man fall off a cliff to his death once.

Any help finding these stories would be much appreciated.