First let me say that I hope I'm wrong, but Heller et. al are throwing lots of clues toward Red John being Jane.

In no particular order, here are some reasons, and you can decide for yourself if these are bogus. They might be.  I hope that they are--that they're red herrings. I'll start with the ideas and follow with possible debunkings.

- Jane reads a lot of Jung.  He is seen in several episodes reading books by Carl Jung. One of Jung's theories is the idea of Individuation:  Combining the conscious (Jane) with the unconscious (RJ).  

    debunk (?): Jane often says the subconscious knows things the conscious self doesn't know.  While this could work hand-in-hand with the theory that PJ is RJ, the fact is when Jane hallucinates about his daughter she doesn't accuse him. This may not matter, however, since she was wrong about a lot--she led him to the wrong killer (the assistant). He could have been in a shallow state of hallucination, not completely Red John. Going along with this, when Jane "loses" his memory he doesn't suddenly turn into a serial killer type. Though he does, let's note, end up at the end with a girl dressed in Red.

- Tyger, Tyger.  This is RJ's "signature" poem with Jane. Its companion poem is "Little Lamb," also by Blake.  The two are meant to be opposites, juxtaposed halves of one, Innocence and Experience, which is threaded throughout all the work of Blake.

    debunk (?): Just because the poems are opposites doesn't mean they are at work within Jane.  Maybe RJ sees Jane as his opposite, and Jane sees RJ as his opposite, etc. 

- Jane regularly makes the point that the perpetrator of crimes likes to be involved in the investigation (see James Panzer, the cop in the episode with the lottery ticket, etc.) Jane himself is always very involved in investigations involving Red John.

    debunk (?): coincidence.  Lisbon, et al. are also involved in investigations that doesn't make them Red John.

- Lorelei looks at Jane when he pulls up to pick her up. She says, disappointedly, "You?" but only after a beat.  As if something about Jane told her he was in his "PJ" mode.  

    debunk (?): It could have been just surprise. We don't see her face at the exact second. Her "shake hands" comment later suggests Jane and RJ are distinct individuals. But this could easily be a misdirection purposefully said by Lorelei.

- Darcy.  Susan Darcy, when she begins questioning Jane about his affiliation with Red John, gets a bit of a rise out of Jane.  He never explicitly denies that he is Red John, though he says he is not a friend or disciple. 

    debunk (?): coincidence. Without suspicion the scene could just play out straight and Jane's words could all be taken at face value.


These are only a few clues I can think of off the top of my head, but now I can't help looking for more. 

Now evidence supposedly against Jane being Red John:

- He wasn't at home when his family was killed. 
    debunk:  We don't know this for a fact.  His family could have been murdered at any time. The sequences where he finds the note are ALL FLASHBACK MEMORY SEQUENCES. Jane's "memory" is unreliable.

- Patrick Jane "meets" RJ when tied up in cellophane in the chair during the copycat film.  
    debunk:  The man in the mask was Timothy Carter, utilized by Jane to "protect" him and play Red John when necessary. RJ routinely uses others to kill for him (like Rebecca who kills Bosco and his team.)

- Various people who know RJ are out to get or otherwise interact with Patrick. (Dumar, Rosalind, Rebecca, Lorelei, Todd Johnson, O'Laughlin).
     debunk: These people presumably know Red John and know of his occasional "lapse" into PJ mode. Hypnosis or some other mandate to not reveal to PJ the truth could be involved.

- We've seen Red John sipping tea, etc. when Jane was in another room.
     debunk: There have been at least three misdirected Red Johns: Linus Wagner in the pilot, Timothy Carter, and the two teenagers who were copying Red John's style of killing.  There are also many people "in league" with Red John. The person sipping sea could have merely been one of them.

I'm done.  I HATE the idea that PJ is Red John.  Looking for good evidence against it, if you have it.

Cheers.