In the End
In the end it doesn't matter that he was a great hunter, that he had saved hundreds of lives. In the end it does not matter that he had done and would still do if he anything to protect his family. In the end it doesn't matter that it tormenting him inside seeing all their suffering, for there is nothing he can do but stand there and watch. If he could die again he would be willing to die to stop their pain but there is nothing he can do but stand and watch.
He watches as his oldest tortures himself over his death and his parting secret, while his youngest is clueless and unable to understand what is wrong. He watches as his oldest takes a swing at his youngest but his youngest never retaliates. He watches as his oldest locks himself in a hospital room with his youngest, even thought he knows the youngest is cursed. He watches as his youngest has to kill a young woman he fell in love with while his oldest listens from next door. He watches as youngest dies in the arms of his oldest. And yes he is watching when his oldest sells his soul for his younger brother.
Finally he gets a chance to do more than just stand and watch his children suffer, he can once again do the one the thing he has always tried to do for his children, he can protect them, as he takes the demon head on all he thinks about is protecting his children, Mary's children. Nothing matters more than them being safe, them being alive.
In the end it doesn't matter who wasted yellow eyes it is that he is finally gone. Looking into Dean's hazel eyes he feels such pride for both his sons that he feels he could die all over again. But there is another feeling slowly tearing him inside, that of where Dean is going and what will happen to him. Once again there is nothing he can do to help his son, he can't even stand and watch. Taking one final look at his beloved sons, John Winchester disappears forever.
In the end it does matter who you were or what you have done.
In the end, it is the end.
But is it? When you are in the hearts and minds of those who loved you.
In the end thats all that counts.