I believe that Red John is a combination, or cell of characters that all take a hold around Jane. The most likely (individuals) are Bret Stiles or Kristina Frye; Bret is a man with a God complex. (As pointed out in other "cases," he loves red, and runs a cult. He's screws with Jane at the worst possible times...
  Kristina Frye was his soon-to-be girlfriend before she was abducted. She was traumatized beyond speech... She was a "psychic" and told Jane that his daughter didn't suffer. This show is never going to allow an actual Supernatural factor, that would undermine the whole plot. She was there.
  As a "RJ Cult" Member, Grace Van Pelt *could* be part of it as reconnaissance. As pointed out in other cases, we know very little of her. Grace was new to the team soon-after Jane joined.
  Another theory (indirectly) points out that Jane could have severe MPD (Multiple Personality Disorder) and be Red John himself... I find this *last part* incredulous because there are no seemingly long absences between them. However, it could be compared to "Fight Club," the leader of Fight Club was regarded as a demi-god.. He didn't know it until the climax of the movie.
  Red John may be attempting to drive Patrick Jane mad, so he could take over the "Jane body." His Cult would follow him blindly and do what they could to drive Jane mad... I think this is the most likely twist, one person is not enough for such a masterpiece, it has to be at least three people... 
 Please speak of any points and counter-points that come to mind! Thank you for reading!