Ok, so I have two theories that I've been toying with.
The first is that Red John is not one single person, but an idea used to enact the goals of the mysterious group who use the phrase "Tiger Tiger". Essentially, all the people in the organisation are Red John and also none of them if this theory is correct. As a clandestine organisation, the group would have the resources and abilities to pull off everything that Red John does. They could have created this character of Red John as a smoke screen to hide their crimes through misdirection, and also as a threat to those who would cause them harm. While the police are looking for a singular person they believe to be a mass murderer, the group are able to cover up their crimes and continue to operate in secret with little fear of being discovered, because the police have never even thought that it could be more than one person. A member commits a murder, and then uses the Red John symbol to send the police chasing after a ghost while they continue with their lives. I could go into far more detail on how this would work, and why I think this might be the case, but I think it's obvious the angle I'm looking at this from.
The second theory I've been entertaining, is that Red John is not a member of the group who use "Tiger Tiger", but is in fact their enemy. In the episode where Jane is captured by the wannabe Red John disciples and is rescued by Red John, Red John says the words "Tiger Tiger" to him. What if, instead of him using the term to show his affiliation, he said it as a warning to Jane, giving him the first hint of the existence of the group. It has been suggested before that Red John is trying to recruit Jane as one of his disciples, what if the reason for this is that he is fighting a secret war with this group of corrupt law enforcement agents? Red John could very well have killed Jane's family to push him towards a life as a crime fighter, to encourage him to seek revenge and justice. This entire story of Jane's hunt for Red John could just be Red John training Jane to be a weapon against the Tiger Tiger group. It could even be the other way around, and turn out that Red John did not kill Jane's family, but that Tiger Tiger did and used Red John's mark to send Jane after him. Both are cunning, resourceful and far reaching enough to pull off a plan of that scale.
A third point of note, although this isn't really a theory is the constant referencing in the show to the question of do psychics exist? If it were to turn out that in the world of The Mentalist psychics do exist, then this would add a very interesting element to the game being played by the factions in the show. Throughout all the series, it has been very unclear where everyone's loyalties lie and who is on what side of the game, and I can't wait to see how it all turns out.
Hope you enjoyed reading my theories, please contact me if you wish to discuss them further.