My spoiler free thoughts on where Supernatural is taking the Bobby story.
I've been thinking about ghost!Bobby a lot, even before we had confirmation that Bobby is a ghost. The hints they've left in the show haven't been subtle at all, though when you bring them all together, it does paint a more complete picture. Maybe I'm off or maybe I'm on. We'll see.
Anyway, the Reaper gave Bobby a choice: stay behind or stay as a ghost (and risk the chance of becoming a vengeful spirit). We've seen examples scattered through the season: Dean's beer vanishes, the paper that mysteriously presents itself when Sam and Dean needed Bobby's help, the sword flying into Dean's hands...I am sure there are more that I am missing. They finally revealed all these occurrences were Bobby and that he is attached to the flask.
My guess is that not only is Bobby haunting the boys, but also that Dean is channeling him. Why not Sam? Back in the Season 2 episode In My Time of Dying, when Dean was a spirit and faced with the same prospects as Bobby, Sam was able to channel Dean due to their closeness and his psychic ability. Here, Dean is the one who is always carrying the flask. I think keeping that item on him is influencing him. If Sam was carrying the flask I would assume it would be happening to him.
I would assume Bobby wants revenge on Dick for killing him. Dean seems to have an unhealthy obsession with Dick right now. (Though it can be argued that Dean is just revenge-driven because it was a loved one who died.)
In one episode, Dean spoke Japanese. Bobby has been shown to speak Japanese. (Though, we've seen Dean say words in other languages before.)
I thought there were more examples, but I can't think of them right now. And yeah, these examples aren't strong and can be interpreted different ways. I'm just going by what I think.
So I was thinking, what happens next? If Bobby starts to become more and more angry, would that channel through Dean? Would Bobby and/or Dean go postal? Would it cause problems for the boys? And if they learn about Bobby, what will they do? It's no accident that they chose Sam's solo case at the psych ward as a loved one turned angry spirit. That girl's brother's presence was comforting at first until his loneliness overcame him. Can we expect something similar for Bobby? I don't see him going off to kill Sam and Dean so they can be together, but if he is turning into a vengeful spirit, that is bound to be a problem.
(I say this with the understanding not all spirits go evil. Think episodes like Home (Mary), and the spirits in Roadkill and The Usual Suspects.)
But the show has set the foundation for some of the main characters to go in the direction of revengeful. It was Tessa's whole part in In My Time of Dying that really piqued my interest in the show. About how Dean could become the very thing he hunts. He could have ended as an angry, frustrated spirit haunting the halls of the hospital. Maybe Bobby is heading for a similar fate.
I am excited and nervous where this story goes. Hopefully there will be some twist. But even if we get a heartbreaking end where the boys have to put Bobby's spirit to rest or he chooses to rest himself, I'm sure it'll be fantastic.