Some interesting theories floating about here, here are some of mine:

1) It is NOT Brett Patridge, he seems weird but is not even close to having the influence, power, connections to be Red John
2) Brett Stiles would be a good fit but I think he is too old (also he has always wanted to help Jane e.g. finding Kristina Fye and getting Lorelei Martins out of jail)
3) It is not Ellis Mars or CBI Ron (same reason as Brett Patridge as they do not have enough power and prestige and Ellis Mars seems really stupid and was easily exposed as being a fake psychic)
4) It is not Walter Mashburn, he does have power and influence but i think he lacks the mental capacity and evilness for being Red John.
5) Dean Harken could be a good fit as he has power and influence and also seems to be smart but he was easily fooled by jane's plan in the bio-chemicals episode so I am not sure.
6) Director Bertrand and Virgil Minelli have always seemed kinda mysterious to me and not what they appear to be. I think they are NOT Red John as they do not match the physical description and age of him but I believe they may be accomplices or somehow connected to him.
7) Bob Kirkland is really popular as a choice to be red john among followers of the show but I do not think it is him, it would be too obvious although I do find it weird why he is obsessed with Jane and red john so i think he may be an accomplice trying to cover red johns tracks as he may suspect jane is getting close to figuring out who red john is (he might have gotten jane's research to study it himself and see if red john has made any "mistakes", clues or trends which he would then tell red john about to not repeat it)
8) Ray Haffner could also a good fit for red john as he is a senior member of the CBI and is quite smart himself (starting his own private agency). I honestly do not know too much about him to make a prediction
9) Van Pelt has also seemd mysterious to me from the start, Jane mentioned that she suffered a past trauma as a child and her sister commited "suicide". I think there is more to her than what the show has already shown. I do NOT think she is red john but she could be a long term undercover accomplice or something.
10) Oscar Ardilles has always seemed antagonistic to me so he could be Red John, he is resourceful and seems to be intelligent. Plus his name O Ardilles is an anagram for "a soldier" and Lorelei mentioned that Red John sees jane as "comrade". Also, "Cut Iron" is an anagram for "in court"
11) It is NOT Patrick Jane's father either, he is smart (taught jane everything he knows) but probably is not resourceful enough and would not ruin his son's life by killing his own granddaughter and daughter in-law. Plus he would be too old
12) One interesting theory I have is that it could be Jane's twin brother or something that even jane does not know exist (in the show, NOTHING has ever been mentioned about Jane's mother). The twin brother could have become bitter about Jane's success as a psychic and for be estranged so he exacted revenge on him by killing jane's wife and daughter and being a serial killer. This would explain his intellect.

In summary, I think the best bet for Red John could be Ray Haffner, Oscar Ardilles or someone from Janes past carnival life like a twin brother.

Thoughts?