My theory is this.

This whole show is a dream of some sort that Patrick Jane is having.

I think Patrick is actually still in the mental hospital from his mental breakdown from his wife and daughters murder and he is delusional.

It just seems so impossible that one man, Red John could be behind all of this. 

I really dont hope this is true though.

If this was not true, I would have to say that Red John is Ellis Mars. The actor that plays him, John Billingsley, has played serial killers in other shows such as Cold Case. He also has a high fucking voice. Another reason is because of the HE IS MAR shit. 

Another reason for Ellis Mars is that the episode he was in, "RED MOON". Mars, his last name, is referred to as the RED PLANET.

idk, but im still sticking with my first theory.

This is a little complicated, but I will try to simplify it as much as possible.  There was a man who called himself Red John, and he was a serial killer.  He is responsible for the deaths of Patrick Jane's wife and daughter.  Wracked by grief at their deaths, Patrick sought out Red John, found him, and avenged his family by killing him.  This, however, is only the beginning of our story.  You see, Jane is a man who no longer has anything to live for.  His only purpose in life was vengeance on his family's murderer.  Unable to survive now that his revenge has left him empty and unfulfilled, his mind breaks.  He creates a new "Red John" in his mind.  Although Jane is unaware of John presense, it is unclear if John is aware of Jane.  This new personality gives him a purpose and reason to live again.  His dual persona has a second purpose though.  Red John was not just one man, alone.  He had a large network of followers, with members embedded in multiple facets of society, including law enforcement.  By living on in Patrick's mind, this new "Red John" can be used as a tool to smoke out the real Red John's associates and eradicate them.

We only ever see Patrick when he is conducting investigations with the CBI.  What is he doing with the rest of his time?  He seems to be only part of a life, stuck in a moment in time.  Same clothes, same shoes, same car.  He is not fully invested in his own identity any more, because the new "Red John" is very demanding of his time.  Setting up traps to reveal RJ's disciples.  These are most likely people who have never met the real RJ in real life.  Patrick can arrange meetings through other followers, so as to protect his identity.

At the end of last season, it is clearly Simon Baker's voice we hear as "Red John" converses with Patrick.  The timing of the conversation makes it possible that this was a prerecorded message.  Wainwright's silhouette combined with Baker's voice is a tool to throw us off.  You are trying to match the voice to the image, so you don't realize that it is Baker speaking.

The writer's give us other clues to the truth that exist purely as clues, with no basis in the story.  Patrick Jane and Red John are like two halves of a whole.  Yin and Yang.  Patrick is an effeminate man.  Afraid of violence, he only acts confrontational when he has others to back him up.  He drinks tea, and is generally "soft".  Whereas Red John is the violent, masculine, confident half of the pair.  "John" and "Jane" are clear masculine and feminine opposites, and if you search for colors attached to the name "Patrick" (aside from green associated with Saint Patrick's day, which is more an association with Ireland) you will find the cross of Saint Patrick.  It is a red cross on a white background, eerily reminiscent of Red John's signature red smiley face on a white background.

While some are hesitant to accept Patrick Jane as Red John, it should be noted that the only deaths attributable to Red John since the deaths of Jane's family have all been very bad people.  They have either been disciples of Red John, guilty of murder themselves, or other murderers like the San Joaquin Killer (James Panzer).  Therefore, Patrick is not directly responsible for the deaths of any innocents.

The only true way to destroy a man is to destroy his legacy, what he stands for.  For Jane, killing Red John wasn't enough.  He had to cut out the entire cancer, and destroy his legacy.  The only way for Jane to achieve this was to become Red John, himself.

This isn't really a theory but just what I thought was an interesting remark by Lorelei in the episode "Red Sails in the Sunset" where Jane breaks her out of prison.

Just after Jane shows her the crime scene photo of her sisters murder, she says something along the lines of "you will never convince me Red John murdered her."  At first I was thinking it was something somebody who's brainwashed would say, but I don't think that's actually the case.  She says it with far too much conviction, so much so that it's like she actually KNOWS that Red John could not have raped and killed Miranda.  If you take that at face value, it leads to some interesting points.  Was she:

1.  With Red John at the time the murder took place and both of them nowhere near the crime scene.  Basically she's his alibi.

2.  She was AT the crime scene and saw who committed the murder (herself even).

3.  She knows that Red John is physically incapable of raping a woman.  Would that indicate that Red John is not actually a man?

There's probably a dozen more questions we could raise from that statement!  My theory: it's either Jane (that conversation in the car at the end of season 4 really sounds like Jane changing his voice) or there is no actual Red John, it's more a group of murderers.

Another thing.  I can't remember if Lorelei ever refers to Red John as a he (I'm probably wrong).  The "shook hands" remark seems to deliberately not mention gender.

For me the Red John Killer is Patrick Jane's unconscious, that for me it's different from a second personality but it's the real and hidden jane's personality, making it something new and not another "fight club". (Sorry for my english but it's not my first language)
As I heard in the 5x08 episode, Patrick and Red John met I felt this impulse to investigate who Red John is, so I went online and look for fan theories or usefull recaps, when I happened to find this page my first suspect was JJ Laroche because he's manipulative (he bahaved that way with Rigsby, Vanpelt and Lisbon) we also know he has a dark secret that must be terrible, he has a soft voice, and as Lorelei says they didn't become lifelong friends as they met while with other suspects Jane has a much better relationship. But here I read another user's post where he named a book by C. G. Jung "The Red Book" so I got information about this: it was released for the first time in 2001 (and published in 2009) as Jung's heirs refused to make it public, the book is about an experiment he did, a voluntary confrontation with the unconscious, through active imagination tecniques (something connected with meditation or I suppose self hipnosys). This could be the key to understand the obsession with the red color, and as a second reference in the last episode of the 4th season Jane's reading a book by C. G. Jung, I must add that the release of the book to academics in 2001 matches with the time should take to develop a plot and film a pilot episode in 2007/2008.
After reading this I begun to connect the odds, for example no RJ follower harms Patrick, the only person Patrick kills is a RJ copycat and the only one who claimed to be RJ (his wife was convinced to be married to red john) so he was the only copycat Patrick's conscious would accept to kill without a breakdown, than Simon Baker has a strange eye's cut so when he smiles the RJ logo seems a "ghost like" caricature of Patrick. More clues are given by Lorelei che calls Patrick "my love" in interrogation room, and when Patrick picked her up outside the prison she look into the car approach the door with an happy attitude and only after Patrick speaks she shows delusion, this means she was not able to tell he was not RJ just by the look, than when she only gets angry when she discovers Patrick made every one to belive she kidnapped him but when he tells her RJ raped and killed her sister she just wants to run away from Patrick.

@Parisss, your theory sounded pretty good until you said Det. Marco Francis is a lot like Jane. We haven't seen more than 1minute of this guy, he hardly says a word about anything but the murder and we see no more of him. How you can assume he's a lot like Jane is puzzling. He also looks too young to be RJ. Red John has been a serial killer for 30 years.

None the less, still a good theory I suppose.

The writers of this show are some of the best ever. Everyone seems to be second guessing themselves and also everyone in the show is a suspect! Heller said "Red John is just a man". There is no defining characteristic, hence why we assume it can be anyone.

My assumption is that Jane is RJ, or he knows exactly who RJ is but refuses to tell himself

I'm not really sure that I really believe that Jane is Red John, but after watching the last episode 'Red Sails in the Sunset', some of the theories really got me thinking about how Jane could potentially be Red John without even knowing it. Whenever Lorelei is walking and Jane pulls over and she is surprised to see that it is Jane and not Red John.. I think that she was not surprised to see Jane, but moreso surprised that he was in his Patrick Jane persona as opposed to RJ. If Jane is actually RJ, it would explain how Lorelei was so comfortable with him when she meets him last season in Vegas, she doesn't quite seem the type to sleep around just because Red John tells her to. I think that Lorelei is in love with RJ/Patrick... that's why she is at times so conflicted when taking to Patrick.. and she refuses to believe him when he tries to tell her that it was Red John that raped/killed her sister because then that would be mean it was Patrick... she also does not seem overly worried about Red John finding her upon her escape from prison, and also passes up on numerous opportunities to take the car and leave Patrick behind. I know this is kind of a mess because all these random thoughts are popping into my head but it is somewhat making more sense to me as I go along. Lorelei is also genuinely disappointed when she finds out that Patrick had somewhat been planning her(why she attacks him) because she thought that maybe he seriously intended for the two of them to actually take off and be together. This also would explain why she will never tell him who Red John is, because she could never bring herself to tell him the truth... but also why she tells him they are basically the same person when she is frustrated with him. I think the episode indirectly focused on the fact that Lorelei has to interact with Patrick and Red John, being in love with both sides which is why she will virtually do anything that RJ or Patrick tells her to do.

£1000 on Patrick to be RJ and Van Pelt is his lovely assistant. Or as Jane likes to put it, the beautiful assistant that creates all the distractions. How many times has Jane got her to go places with him or convince her to behave "sexual" to get information from people?

I had written an essay earlier on my theory but for some reason it didn't post so I kept this brief as I really don't write it all out again.

I just rewatched every episode and analysed every last detail about not only Janes character, but his quotes and what he knows about Red John.

We all think Red John is steps ahead of Jane, but in the end, Jane always seems to know his next move and who he will go for. Hes fighting with this evil inner self and can't cope under the stress its caused him. Hence why he feels unbelievably guilty for his families death. 

The FBI are smarter than they look, they've been onto Jane for a while but now the national security are closing in on him. Ever asked yourself why Jane never looks disturbed when people die? He has purposely got a number of people killed.

All the William Blake stuff is directed at himself,
"Tyger Tyger burning bright,
In the forests of the night"
- Tigers can be vicious, burning bright as in being very visibly angry, in the forests of the night could relate to his insomnia, he's up all night doing only he knows what!

The rest of that poem is him talking to himself. We can also not be sure that in the season 2 finale it is Red John behind that mask, maybe its Van Pelt? Red Johns character would not use a gun, Van Pelt is skilled with one.  She is also not the weakling, so able to pick him up. And definitely has the inner rage to kill people.