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.

I think no one from the List is actually Red John, but Dean Harken(some information there are in my previous post). But I think I wasn't clear enough. Now let me tell you why the list is wrong:
Bret Stiles: Jay Roth was in his 50s, Stiles is 70

Bret Partridge: Dead and Buried. We saw his corpse, so no faking of death. Sorry.

Robert Kirkland: By the looks of Episode 4 Promo, he simply wants to know who Red John is. We know he already has a fake list, plus, he got that list 2 Months AFTER Lorelei was murdered, John had it before she was murdered. Plus, don't forget:
 This is the first debut of Robert Kirkland’s
character in the TV Series. In episode 2x08 “His Red Right Hand”, Kirkland
appears briefly (and un-identifiable) after Virgil Minelli finishes his speech.

After what may have been, an off-screen meeting,
Minelli resigns even though he told Lisbon earlier that day that he would never
give up.

Minelli is replaced by the most capable, Madeleine
Hightower, ex Intelligence Agent in Fresno, CA.



Gale Bertram: He supports Kirkland, he is bald and he is waay too tall, so he can't be. I think Bertram is a multi-functional Red Herring that Heller uses every time he needs.

Reede Smith: Red John has to be really cold-blooded. Smith is the opposite, very brutal, very violent and very stupid. Red John's high self-esteem and idea of nobility(classic music) wouldn't accept to pick a public fight with CBI Agents. Plus, he's in league with Bertram and McAllister. He wants to capture John.

Thomas McAllister: He allied himself with Bertram and Smith, he saved Jane and he's really a secondary character. There is also no phobia of birds, just a natural reaction to a bird flying in his face. Most likely Heller knew that the community would think of Ornithophobia after the first 2 episodes: Admit it: He was expecting you to think of pigeons!

Raymond Haffner: Haffner is not the brightest of the Suspects. Red John wouldn't need Cho to spy on Jane, and also, he would have recognized Jane's writing in the Notebook. On short words, he would not have been fooled on S04E02. Plus, we know Red John's strongest point is his persuasive ability, while Haffner has a very bad relationship with Teresa, doted to the lack of his Persuasive Skills. And it becomes too obvious in The Red Barn, when Lisbon asks Haffner if he was in The Barn at that time. John would have lied to her right in her eyes. However he may be Red John's mole inside the CBI, else, how could John enter the CBI Intranet?

THE RED HERRINGS: Whistling and Lisbon's Dream are more Red Herrings. This kicks out Bertram, Smith, McAllister and Haffner. We see Haffner Whistle and cut Lisbon's throat, a very typical Red Herring from Heller. Same works for Reede Smith, he whistles+he's in the dream. Bertram paints the smiley, and McAllister whistles. Red Herrings my friends.

So, I'm sorry, but I think we have to point someone else. I insist on Harken: Why? Because every point of evidence leads to him. I made a compilation of Evidence that point to Harken:


-        
Dean
Harken is 43 years old, just under 6 feet tall, with short, straight hair, a
soft voice and an odd Scottish accent.


-       
Dean
Harken has a private army/private security, which means he is very influential
in terms of Money. Red John is too. This gives Dean Harken access to many
places via his followers. Note that Patrick made the List of Seven supposing
that Red John has direct access in all those places. He forgets that John needs
only one of those guys from the list either as disciple, either corrupt to gain
“access”. I bet it’s Ray Haffner, Red John’s mole inside the CBI.
-        
Dean
Harken is skilled in informatics. Red John is too since he has access in the
CBI intranet. Again, this may be doted to what I suppose is a partnership with
Ray Haffner.(See my file on Raymond
Haffner)


·        
Dean
Harken has Red Hair. Macbeth(historical) got the name of Red King(Ri Deircc)
because he had red hair.


·        
Dean
Harken is married. So is Red John. Both have rings in their finger. Most likely
to Rosalind Harker. Most likely they are not married officially, and Rosalind
got the name of Harker, not Harken. This way, if Rosalind is married to RJ no
one can track this, because the wedding is not legal and the change of last
name is done by one part only.


 -       
Patrick
can’t stand for Harken, he calls him a person who likes “Scared People”. Harken
too seems a little uncomfortable with Jane and Lisbon around. If he was John,
be may have been worried Patrick would identify him.

·        
Dean
Harken has friends at FBI, at least that’s what he tells Patrick. Friends,
plural, more than one. In the 4th season, 24th episode,
Red John mentioned he had a friend at the FBI. But at the time of Season 2,
John had two friends(Craig O’Laughlin too). Is it possible Dean Harken, a
suspect for being Red John, had more than one friend at the FBI, just like Red
John? For me it’s too much a coincidence.
 -        
Dean
Harken is very cold-blooded in his investigation, Red John must be cold-blooded
in all those homicides.
 -        
He
says that requested CBI’s help himself. Why? Why the CBI? Why not the FBI
where he had many friends. Why, unless he wanted to meet with Patrick, what
other motives could there be behind that?



I KNOW SOME OF YOU THINK IT IS NOT PROBABLE FOR HARKEN, BUT, FROM ALL THE PERSONS OUTSIDE THE LIST HE IS THE ONE THAT CONVINCES ME MOST. THOUGH MASHBURN AND ROYSTON DANIELS WOULD BE GOOD ALTERNATIVES.