The Mentalist/WMG

New WMGs at the bottom, please.

Red John is actually a Patrick Jane personality
There has been a lot of focus on how they are very similar. And then the fearful symmetry. And in the season 1 end, the sheriff dies making a "shuuus" gesture, as if telling Patrick "I'm keeping your little secret...".

He suffers MPD and he is Red John. He uses a lot of people to dissimulate this.
 * . Still, it would be an interesting twist.
 * Obviously,
 * I've just noticed that Channel Five (In the UK) has just started advertising for Season 3. They use clips of the Season 2 finale with a voiceover of Kristina Frye speaking lines from the finale. As the clip focuses on Jane tied to the chair the following words flash on the screen one by one: Has he lost his mind. Now sure it could just be advertising or it could be a little bit more support for this WMG.
 * PJ and RJ are very similar initials. All you do is add one more stroke of the pencil. As are Pat Jane (two girls' names) and Red John (a masculine pseudonym a child might think is cool).
 * According to Red John's ex-lover, he has short, straight hair. Jane doesn't.
 * It could be that Patrick Jane as we know him is a Red John personality that was created by his subconscious disgust of who he is, and wanted to have a relatively normal life. Red John was unaware of Patrick's existence until his condemnation of Red John... now he knows, and both sides of himself are fighting each other. A part of Red John wants to be caught, and he eventually will be but not before enjoying the thrill of it all as much as he can. What better adversary can you have but yourself?
 * According to Red John's ex-lover, he has short, straight hair. Jane doesn't.
 * It could be that Patrick Jane as we know him is a Red John personality that was created by his subconscious disgust of who he is, and wanted to have a relatively normal life. Red John was unaware of Patrick's existence until his condemnation of Red John... now he knows, and both sides of himself are fighting each other. A part of Red John wants to be caught, and he eventually will be but not before enjoying the thrill of it all as much as he can. What better adversary can you have but yourself?

Red John is Kristina Frye
Or at least, I for one really really hope so, because otherwise this show has a major hole in it; Jane, like Reality, repeatedly denies that there is any such thing as a psychic. If Kristina Frye is, within the fictional world, genuinely psychic, then the show has contradicted its previous line; but if she is faking it (perhaps somehow fooling herself into the bargain), then she is quite capable of lying to Patrick about it - and has also demonstrated a gift for manipulating people. As per the Fearful Symmetry description above, she could be regarded as a reflection of Jane.
 * Under this WMG, she manipulated him into dating her at the end of season 2 in order that he would form an attachment to her, enabling her to torment him further by disappearing in the finale.
 * I had a similar thought and hope it turns out to be true as well. But I also had the thought that it might be a double twist. Kristina Frye is just another one of Red John's acolytes and Patrick Jane is Red John.
 * Kristina Frye is Red John. Why? She told Jane in Season 1 that his daughter never woke up, and died peacefully. She can't be genuinely psychic because Jane has said over and over again that it's just good reading of people. But there's no way Kristina could have known about Jane's daughter by reading him - she had to have known.
 * ...or she's bluffing. If no one but the killer could know that, who's going to contradict her? And if anyone besides the killer could know that, like the police, then there are dozens of ways the knowledge could leak out. It's not a strict choice between "she's the killer" and "she really is psychic".
 * I'd be inclined to assume it was a lie. She could have easily guessed that that was eating at him, because how could you lose a child and not wonder if they were afraid? It was obvious which answer he would be hoping for, and she told him exactly what he desperately wanted to hear. 'Psychics' work as much because their messages are compelling as because they're convincing - making people want to believe you gets around a lot of skepticism.
 * The part about Jane's daughter might be a kind lie and Kristina's other 'psychic' messages could be from cold reading, which she might be doing subconsciously, genuinely believing herself to be psychic - apart the conversation with the waiter on her date with Jane. That was so specific that it can only mean either (a) Kristina is genuinely in contact with the dead or (b) Kristina staged the whole thing. Assuming for a second that the writers haven't decided to make real psychic powers exist in canon and Kristina staged it - why would she do that? If you're a con artist on a date with someone you know really hates fake psychics, it seems like an odd moment to try and convince him you're the real thing... all it seems to achieve, in fact, is introducing the phrase 'roll tide' so that Red John can say it later to imply he's kidnapped Kristina. Which seems kind of convenient.
 * I really, really want Kristina Fry to be Red John, mainly because after two episodes I'm liking her more than Lisbon of the two 'Jane' ships and I'm not very happy about it (and the scene in the restaurant when her and Jane were on a date was just too dense for the likes of someone with her intellect. It was obviously meant to mean something).
 * Also, for the person that said they thought Jane was red john: Isn't it creepy that red john's smiley face with the sleepy eyes looks alot like Jane? most of the time anyway. the one on his bedroom wall, for example, did but there's a lot of times where the face changes into a normal smiley. to off put us maybe? i hope he isn't red john, though. i really wouldn't be able to watch the series again.

All wrong. Red John is actually the forensics guy.
The voice tone of Red John in the last episode of season 2 is the same as the forensics guy. The creepy one whom Jane says enjoys his work far too much. (This troper is EXTREMELY good at voice tone and frequency recognition.) It's most obvious between the Forensic's guy comment on "Hurry it up, so my team can come in" and Red John saying the word "me" towards the end of the episode. There's a certain tonal constant between Team and Me which matches.
 * Actually, that forensics guy, Brett Patridge, appears in the Pilot as well. That being the case, the writers can avoid Ass Pull since they can just say, "Hey, we already give it to you in the first episode!". This video supports this theory.
 * Both cases that Brett Partridge worked on were cases dealing with Red John Imitators. Makes sense, seeing as Red John hates cheap imitation.

Red John someone we've never met before, and never will meet until the last episode
By either lack of creativity, fear by the producers that if it actually was one of the characters we've met, or fear by the producers that if they decide on someone being Red John early on, and the actor declines to work for them for the final episode, no one who actually controls the plot or creation of the series actually has someone pegged out as Red John. And when he is revealed, it will be an actor that has never been shown on a single episode of the Mentalist (or maybe the actor from the Season 2 finale, but not necessarily since he was more covered than an eskimo) before the series finale.

Psychic abilities exist in-story.
So Jane himself wasn't one; it does not logically follow therefore that none exist. Also, it's either that or some really convoluted explanation for Kristina.

Or Jane really is psychic but is in denial, and uses his considerable intellect to explain his own leaps of intuition to himself.

...and when Occam's Razor postulates that psychic abilities exist, and the main character has repeatedly denied it, you've got one twisted-up show.

Psych is a TV show in the Mentalist-verse
The only difference is that Jane doesn't watch TV, while Shawn does.

Red John is the waiter

 * The waiter is big enough to be a guard in law enforcement, and so sociopathic that Jane doesn't even get a bad vibe from him. For once, the storytellers are being honest with us.

Something significant happened relating to Red John 8 years prior to Season 2.
At that time: My guess, these events are connected.
 * Red John makes the mistake of killing Carter Peake.
 * Minelli takes over as head of the CBI.
 * Sam Bosco kills someone, a criminal who could not be arrested, and Lisbon helps him cover it up.
 * I second with Minelli--though his correct title is Special Agent in Charge, just below the CBI Director--he has definitely his hand in the Red John conspiracy. In "Red Queen", Hightower reveals to Jane that Minelli, her predecessor, has told her to beware of Red John's MOLES in the CBI. When did Minelli resign? When Rebecca, Bosco's secretary and Red John's mole, kills Bosco and his unit.

CBI Director Gale Bertram is, or may be related to, Red John.
In the aftermath of Hightower affair in "Red Queen", he mentions a poem that's written by William Blake. The scary part? William Blake wrote Tyger, Tyger--the poem that Red John recites in "Red Sky in the Morning".
 * Or is it?

Red John is Jane's brother.
Not much is known about Jane's past, other than he worked at a carnival with his dad. Red John and Jane could have been separated at birth, with Red John living with their mother. Jane doesn't talk about his past, and no mention of his mother is ever made. It's pointed out many times that Jane and Red John are alike, and it's possible Jane knows Red John is his brother and chooses not to share this with the team.
 * Alternatively, Red John is Jane's dad and has just aged really well.

Jane is really Willy Wonka.
No, not just The Wonka. The WONKA. Watch Gene Wilder's Wonka and Jane back to back and say that they're not the same person. Curly blond hair, fondness for waistcoats, sadistic glee in messing with people's heads, and they speak with almost the same inflection in their voices. Especially when they're really messing with people and pretending to be innocent.

Patrick Jane suffered a psychotic break after his family died, and we're just watching his insane delusions.
The entire series is just Patrick Jane in a psych-ward regaling the doctor with his fantasy adventures. Which explains why his insane gambits always work, his team seems to like him even though he's a Jerkass who loves playing mind games, and every episode has 'red' or a synonym in the title (as he's the centre of his own universe, his obsession would be the centre and therefore every episode would be named after his obsession.

The person seen
Come on. We have, who is clearly brilliant and a mastermind, and
 * One thing this has going for it is that one of Red John's accomplices commited suicide for him earlier in that very same episode. Its feasible he sent someone to their willing death.
 * One thing this has going for it is that one of Red John's accomplices commited suicide for him earlier in that very same episode. Its feasible he sent someone to their willing death.
 * One thing this has going for it is that one of Red John's accomplices commited suicide for him earlier in that very same episode. Its feasible he sent someone to their willing death.

At the end of the series, Patrick Jane will find God.
And as per his usual manner, will take thing just a little too far, becoming The FundaMentalist.

Patrick Jane really did kill Red John.
Or at least, he had when the season 3 finale was written, and a major arc of season 4 would have been Jane, stripped of his shield of revenge, actually having to grieve and move on from Angela and Charlotte's death. But then the higher-ups had a panic attack, believing that if Red John was dead, people would stop watching the show, and forced the writers to make it that Jane killed an accomplice, not Red John himself.

Red John Has Never Killed Anyone Him/Herself
Think about it. He has a known MO for using pawns and moles to kill all the people he needs. I don't think he gets his thrills from the killing of people. I think he gets them Charlie Manson-style, he gets them from having other people do his bidding. So that guy from the end of season three really did kill Jane's Family, but as Red John doesn't get his hands personally dirty he didn't actually kill Jane's family. There's no concrete proof that Red John has actually ever killed anyone himself. All the onscreen killings are done by moles, and all the scenes stumbled onto by Jane and company simply fit the description of the profile the police have on Red John. The one person that Red John could easily kill (and assuming you don't think it conflicts with the other WMGs here) is Kristina Frye. He doesn't. What does he do? He messes with her mind. The hallmark of a masterfully manipulative bastard.