Here’s how I think the boys stories should come to an end:
Sam and Dean
After breaking through the chaos created by God (aka Chuck), the brothers could find a way to get rid of him. This could be anything from locking him in Lucifer’s cage to somehow killing him. Maybe the brothers could even realize that by killing God they could completely get rid of the monsters. It’s hard to imagine the ending of this show without the death of these iconic brothers. So, it is possible that the boys realize that in order to kill God they must make the ultimate sacrifice, their own lives. They could end up making that sacrifice and defeating God. Eventually, the show could cut to Sam and Dean in heaven, where both brothers are greeted by the friends they have lost along the way. Sam could even reunite with his old girlfriend, Jess.
Castiel
Now, Castiel has that whole deal with the Empty. However, I don’t think his story should end with him being taken back to that place. I believe the boys will help him find a way out of that deal. After the deal is broken, Cas can then take up the job of being the new God. After all, once Chuck is gone, the angles may need a new leader to take up that position. Who better than the loveable angel who has learned both the ways of the mortal world and heaven?
Jack
It may take some time during the last season for Jack to get back to who he was before everything happened. By the end, Jack could get the chance to redeem himself. After this Jack could be there before Dean and Sam go to take out Chuck. During his goodbye to them, Dean could give Jack both the keys to Baby and his necklace. Once the brothers leave to end their stories, Jack could be seen driving off into the sunset. He could be wearing Dean’s necklace and listening to his music.