This isn't a theory ... I would just like to say that i'm having a couple of problems buying the last episode ...
First ... The list ...
Well ... How could RJ get precisely the same list as Jane???
And how come, in jane's list, there's no one from his carnies days or from his psychic days??
He said that the list had the only 7 people that could have been in every crime places ... Really ???
Nobody from his preview life (before CBI) could have been in every crime scene????
But ... continuing ... In the Red Barn episode, we heard, and so did jane, from a priest that a "kid" was painting the smiling face .... Well that was in 1988 ... So the person would have to be 30 (TOPS) in those days ... Well ... Jane knows this ... but RJ didn't know this ... So i can understand why stiles is in RJ's list ... What i can't understand is why is he in Jane's list ... He is too old !!!!!
And ... Last but not least ... How could ANYONE know that Lily Barlow was a happy memory for jane if he didn't tell anyone?????
I guess he could have told in the carnies days or in the asylum but ... Wouldn't he remember telling??
I mean, really people, think a little bit?? Does anyone know who is and who is not in your memories??
Nobody can know that if we don't tell them ... Not our parents, our siblings or our best friends ...
Because, we all have had several happy moments in the past ... And sometimes we don't even know why we remember one more than another ... So how could someone else do it ???

Oh ... And btw ... Let me tell you what i think about the list...
Bret Stiles - To damn old, not a chance he could be RJ ... And ... Why would he help Jane with the escape of Lorelai???
Would he really risk her telling jane he was RJ ???Gale Bertram - The most unrealistic choice of all ... Really?! He is a federal agency Director ... His whereabouts are always known ...
I mean ... Every federal agency director has a team of full-time bodyguards and is electronically tracked ... So for him to be RJ he wouldn't have to be great ... He would have to be freaking Superman !!Robert Kirkland - The proof that there was never a RJ and they put a guy into the show just to be RJ ... A guy that appeared from nowhere and suddenly has 10 or 12 proof against him in a couple of episodes.Ray Haffner - Precisely the same thing as kirkland ...Reede Smith - my answer to this, and all you super fans will understand, is ... WHO ????? His name had to be one just to make an even 7 name list (7 names, 7 letters in red john)Sheriff McAllister - He is a nobody and he is a bit too old to be RJ ...Brett Partridge - The guy everybody suspected, at least for a moment ... The guy that doesn't make sense because he's too obvious ...I really would prefer if RJ would've been Mashburn, Winter or Royston Daniels ... But ... in this list, if RJ is anyone but Partridge the ending won't be disappointing, it will be stupid !!

Oh ... i remembered another thing ... So ... Jane was head to head with RJ in that tyger tyger stuff and didn't notice that Reede smith couldn't possibly be that man ... i mean ... the whole body is completely different ...
Reede smith is a rounder version of a RJ ... =P)

Assuming that one of the seven is really rj, then it has to be Brett Partridge. Apart from the fact that he was introduced right from the first episode, he is also the only name (out of the 7) that appers on the page of pj's initial agenta of suspects as shown very briefly at the finale of s5ep9. In fact the name is less visible due to the shade of pj's finger, but if you freeze the picture it is very clear.

The list of seven provides so many possibilities to who RJ exactly is. Whether It be a character in one episode or a recurring one, it's interesting to think about who it may be. It's going to be a long summer.

Here's my thoughts:

RJ has killed about 25 people on his own, and I'm sure many others at his request. That's a lot of people for one person to kill, and even more family members who would miss them when they're gone. PJ cannot be the only person who is pissed at RJ...it's just not possible. Therefore, there must be others who want to get him and have atonement, retribution, revenge.

Enter Bob Kirkland.

Bob has lost someone because of RJ and he's pissed, motivated, almost to the point that PJ is, but not quite. PJ wants revenge, Bob is a federal agent, and he wants to catch him like any criminal agent would. He's studied the case for 5 years...he knows it well. He invokes the help of CBI, specifically Gale Bertram, wondering if they can trust PJ with information. He breaks into his room to see how far PJ has gotten without him knowing it. And yes...I think Lorelei is dead and know that Bob broke in after her death. In the end, Bob and PJ might work together to catch him...both motivated to be the ones that finally caught California's most notorious serial killer. Both want revenge; PJ won't kill known accomplices of RJ but Bob will. He has that hatred motivating him. PJ is trying to get his life back and rid himself of the horror.

As many people have pointed out, Bob is too obvious to be RJ...but what I want to know is why a Homeland Security agent is worried about a serial killer. A little out of his jurisdiction. He is more than likely a red herring. But not all herring fish are red, and not all Johns are red. So how did RJ get his name? The public named him...but why John? Why not Tom, or Bob, those are common? Perhaps John is a middle name. Brett John? Reede John? What about Raymond John?

PJ got really paranoid once the list was being whittled down. So he closed his door, worked in secret, let no one in, even Theresa, knowing someone at/with CBI is either RJ or working for him. RJ likes to hack into CBI, PJ knows this, and assumes that at some point, after learning about them shaking hands, his room will be broken into. So what do you do??? You track RJ, or make it look like you are tracking him, setting up data spread over a wall that rivals a neurotic vigilante. You test the theory with the toothpick, hence his elation when discovering it broken in half. And based on what was on the wall, RJ or his "friend" would find out what PJ knows and surmise what he believes is on PJ's list. RJ is always one step ahead of PJ but not this time...PJ has turned the tables, tricking RJ, who tells him the seven names which appear as suggestions of other suspects on PJ's wall. The name RJ also has seven letters in it for the seven suspects.

Interesting to note that all are law enforcement affiliated (except one), are kinda weirdos in their own respect, and are people of high power, which RJ craves. Many of the suspects can be cross referenced to either working together, present or formally, in the same cult group, or are from sister/cousin agencies in the federal government. Makes you wonder who knows what.

PJ's year in incarceration will be the reasoning for the happy memory being effectively pulled from his head. Hypnosis. Either in therapy or in the office. Someone who is faking their day job and is actually a true mentalist, unlike PJ, who doesn't believe in it, is RJ. And I haven't ruled plastic surgery with possible father/brother/family member of PJ being RJ, or the fact that some characters are so little seen on the screen. To me, any of them can be RJ.

PS
My only question is this: I read on here that Bruno Heller once said in an interview that when the show began, PJ was supposed to be RJ. Anyone have that article/link?

My opinion is that Brett partridge is Red John because he stands out too much.

His character has been intertwined with RJ from the first episode of the show. He was put there before most of the script was written, they wanted RJ to be in the first episode, even before they knew how his character would play out. The producers just needed a face at the start of the series, so that by the end of the show, when he is caught, RJ's story would complete a full circle and have a beginning too, not just an end. It's highly unlikely they will chose someone else.

In the list of the seven suspects he stand out by being by far the youngest there, also RJ nominates him last on the cd. I don't think a serial killer like RJ would put himself randomly in the middle of list like some no-name, he would put himself either first or last.

Another thing that I think is a clue is that he always tries to be the buffoon, the joker of the room, trying to grab Jane's attention and always mocking him.
 In the first appearance, in the fake RJ murder, he takes control of the room and quickly proceeds to explain how RJ killed them, "classic RJ smiley face" and declares himself "spooked to finally see one(smiley face) in the flesh", although he obviously knows it wasn't him, he's just happy to mock Jane in plane sight.
In the second murder, when it really was him, he states the opposite, he says it's not RJ. It's not an attempt to lead Jane away from the truth, it would be a very thin attempt if it was, he just likes to mess with Jane by always taking a different opinion. 
In the old lady incineration episode he enjoys making Jane sick by being overly macabre and giving disgusting details because he knows Jane doesn't have the stomach for that sort of things.

Also, when he appears on the two RJ murder investigation, the camera always films him with the :-) showing behind his shoulder whenever he talks to Jane. You can't get anymore symbolic than that. Or can you? The first time we see Brett Partridge is when he explains the path the supposedly RJ murderer took in the house. He walks through the door into the room using himself to describe the movement of the attacker. His first line is "Red John enters here".