I'm going to take one more stab at this after researching for a while. Please leave comments and vote based on whether you think this is plausible or unlikely.

I am accusing Alex Jane as being Red John. I will keep this short and to the point. Here are my reasons (both in the story and from the cast and crew's point of view):
1. Red John is much like Patrick and it is possible that he could be Patrick's former teacher i.e. his father Alex Jane.
2. The episode in which Alex appears, 'Throwing Fire' was partially written by Bruno Heller himself. Bruno usually works on all episodes regarding Red John himself.
3. Alex Jane could have known about Patrick Jane's 'happy memory'.
4. Alex has motive, when Patrick Jane ran off with his wife from the carnival, it is said that his father was enraged. He could have taken revenge on Patrick by killing his wife and daughter.
5. Bret Stiles says he knew Patrick's father, it has been established that Red John was in Visualize long ago. This certainly fits the time frame, as the first Red John murders took place in 1988 and Patrick and his wife left the carnival in 1985. Thus, his father could have been there in 1988.
6. Alex Jane is portrayed as a master manipulator. This could stand as reason that he could gain influence over people in the FBI and CBI. 
7. Alex wears a wedding band even though we never hear of Patrick Jane's mother. Red John, as previously seen, wears one as well even though it seems he could be unmarried. He wore it while having a 'relationship' with Rosalind at least.
8. In the episode 'Red John's Rules', Alex Jane is brought up again as a topic of conversation, Sean Barlow mentions that Alex is a wicked man that exploits others. Red John is obviously a wicked man as well.
9. It is mentioned on many occasions that Patrick and Red John know each other extremely well. How much better can two men know each other than a father and a son.

As far as I am concerned, the only possible flaw in the story would be the handshake comment. Why would Patrick only become friends with his father when they 'shake hands'? That does not make much sense.

However, I feel that Patrick's father fits the clues and I like him for being Red John. I do not believe he works alone, but he is in my opinion Red John.

Please comment. I would like to know if I am missing something that would exclude Alex definitely. But please do not dismiss this without evidence.

Well, this poll below seems to have it nailed - Red John is actually Mr. B!
http://poll.pollcode.com/76818

Why do you press unlikely when its a fact that Simon Baker is playing RJ's voice? Idiots..

People keep saying that RJ's voice sounds like Brett Partridge, sure it does in a way.
But Red John's voice is portrayed by Simon Baker, so yeah there you have it.

An in addition to what PJane99 said in #6081:

The two buttons are called "plausible" and "unlikely". Not "i have the same opinion" and "i disagree". And also not "i like this theory" or "i don't like it".

If a theory is plausible but does not reflect your personal opinion, it is still plausible! Which means the green button :)

     Majio spoilers read ahead at your own risk

For thouse who haven't already seen it yet i have the season 6 episode 4 promo linked
http://www.youtube.com/watch?v=8wp9F6xNX44 Jane very clearly states that somebody is killing people on his fake list! yes i know im as shocked as all of you all this time and effort we have spent on analyzing each suspect has led to nothing. But don't despair all the evidence we have collected has not gone to waste. The fact that the list is fake makes complete sense we know Jane had knowledge of people breaking into his home and he did plant the toothpick in the door so it would make sense for him to not have his real list out in the open for the taking. We also hear from high tower that Jane has been under surveillance for 9 YEARS  that's right a whole nine years from the day he had joined the cbi he was under surveillance from homeland. Someone had ordered jane to be under surveillance from the day he joined. No prize for guessing who my money is on red john but he it could be done by one of his accomplice. In fact this whole idea of the list be fake makes complete sense many of the suspect just don't fit what previous evidence told us. The most famous piece of evidence we have Rosalind description already eliminate 3 out of the 7 suspect. Reed Smith is simply too fat to be red john as Rosalind said red john was Red John is not fat nor strong both are traits of Reed smith. Bret stiles is too old to be red john as Rosalind said red john was of medium age the same goes for Gale bertram also Betram is lacking hair as Roasalind said he had short straight hair this also apply to Sheriff McAllister. Also another point about Bret stiles why would the leader of visualize work on his own lowly farm that was failing don't you think that a job he could of given to some new visualize member like the others at the farm. And Brett Partridge is dead and the list being fake gives us no reason for him to come back so all of you accept it his dead. Now this leaves us with only 2 of the 7 suspects of the list and do you really think Bruno Heller would making finding red john that easy. This also makes alot of sense from a writer perspective it opens up alot more possibility we could see the return of old suspects like Mashburn or even cbi ron. But i personally felt that Mashburn and jane got on too well for him to be red john he let jane drive his very expensive care hardly the act you would do with your mortal enemy. Also i believe cbi ron is just too much of a cheap cop out for them and would had mass back lash. So my money is on Haffner although we see kirkland hold jane hostage i believe this is too mutch of a bold move for red john he isn't even wearing a mask and Haffner is in love with lisbon explaining why red john didn't kill him and he does fit both sophie millers description and Rosalind description so my money is on him.
Although bruno heller did say red john was someone we saw from the start of the show and Haffner is relevantly new in the time line of the show.

Now i have one final topic i wish to discuss and that is what happens after red john is caught we all know that the show is continuing with lisbon,patric and cho all keeping their roles and two new characters joining the team.  If you go on the following link http://www.tvguide.com/News/Mega-Buzz-Nashville-Castle-Spoilers-1071832.aspx and scroll down to the part on the mentalist you see bruno heller explain the meeting of the 3 suspects in episode 2 and he says  "The CBI goes through its own sort of institutional crisis," Heller teases. "The walls are crumbling around them as they are trying to solve this big final mystery. Bertram is both a prime suspect as Red John, but also deeply involved in that other plot." this new plot is set to become the primary focus after red john is caught and reed smith, Mcallisiter and gale Bertram will all take primary roles in this new plot. So my final point is we all know names are important in the mentalist and the name red john. John in particular is from the name John the baptist from the bible who was a great prophet in Christianity but more importantly prepared the world for the coming of Jesus so maybe red john is bruno heller way for preparing us for a greater evil then red john and who greater could take this role then Bret stiles and i want to end this post of mine with a line from Bret stiles; "i know more then you or red john could ever know"

Thank you for taking the time to read this very long post and please click that plausible button so more people can see this and take the time to read it thank you.

My guess is that the 7 suspects are all-in-one Red John(like a seven sins ideea). They are all connected. This could explain a lot: "He is mar" = "He is many"; it explains the list being made ahead Jane's thinking; that has many friends and influence; also one step ahead, present almost from the beginning; some of them members of Visualise or all of them, some of them whistle; they all reveal themselves to others(each to whom they had a connection in the past). Maybe Brett is not dead or had to be cut loose.
Think about this ideea in all the situations that you can not explain(in one can be brett, in one can be Kirkland, in one can be Reed and so on...)