The people that could RJ in my opinion are these (in order of suspect):

-Virgil Minelli
-Gale Bertram
-Ellis Mars


Ellis Mars could be but doesn't matches the physical description (he is quite soft). So... excluded.

Gale Bertram in the last episode of season 3 after Jane tells him that they will meet Hightower in the mall... right when Jane goes out... Bertram makes a phone call. He phones Timothy Carter to set up the trap to Jane? Or phones to RJ so HE can set up the trap? Being or not being RJ he is totally implied (he tells a part of the Blake poem, the newspaper, the tea on the desk) High social status, power, as chief of CBI knows politicians, has friends in FBI and so on. Now I tell WHY he is NOT RJ.
Let's see the show: 
It's a duel between two masterminds. When you start a game, you introduce the players first right? So the first episode introduced PJ and obviuosly RJ BUT! They did it in a mgnificent way, with a fake RJ case so you are unable to figure out that RJ was already been introduced. It's not Gale Bertram, it's Virgil Minelli.

-Virgil Minelli is RJ. The evil mastermind behind everything. He has everything under control till he has to kill Bosco and his team due to give the case back to PJ and Lisbon's team. He makes himself a wayout, so he can control from outside. It's the moment when it becomes a real duel among PJ and RJ. As a declaration of war.

Hightower is one of his underlings and Craig O'laughling knows it. When he enters the chatau and he is discovered he later shows no fear to die so if is mission was to kill Hightower... WHY he jus't didn't kill her? LaRoche is also another member of the gang. he shoots the man who placed the bomb on Lisbon's body, it's shown he waits without a reason outside the car... as if it was planned. Then. He justifies. LaRoche? Why adding that line? Non sense. It was planned.

Minelli is RJ because is not in an highest rank but not in a lower either. Then the last thing:

-Rebecca, when she saw his murder she is overwhelmed by joy. She could feel that way only for RJ. So RJ is in the CBI. Everyone would have noticed Bertram immediately in the CBI. But Minelli? Or Partridge did the handword on his master's orders? That fits. So Partridge killed Rebecca and with Bertram and LaRoche is the third keyman of RJ in the CBI.

When Lorelei told that "shake hand thing" to PJ referred of a situation before her capture, so before season 4 ending. Because later on she was in jail.
So... enough with the "is Robert Kirkland! Is Bob Kirkland!" 
Because Kirkland is NOT RJ, maybe he is the FBI mole of RJ or... is Volkers friend and Volker is RJ's friend wich makes him obviously another of RJ's friends. 

Well thanks for reading my theory. I hope it's uncorrect so not to ruin the final surprise on finding out who RJ is. : )

http://www.zen134237.zen.co.uk/Mentalist/The_Mentalist_1x01_-_Pilot.pdf

That's a link to the original script for the very first episode! The CBI boss is called RJ! Explains it all really.

S3. E10.

Patrick approaches Minelli (Minelli refers to PJ as just Patrick, like Red John does) while fishing and tells him he has the upper hand on Red John. Minelli laughs and says to Jane "You sound nuts my friend". At the end of the episode, we also learn that Minelli has stole LaRoches suspect list to give to Jane.

Virgil Minelli: LaRoche's suspect list. Secured through back channels, and personal favors. LaRoche has no idea I have it.

Sounds like something RJ would do, doesn't it?

S1. E04.
Virgil Minelli: Jane, you close cases. You - you close like a fiend. So I tolerate you and I - I protect you. And I let you make Lisbon's life a misery. But there's - there is -there is a line. And when you cross it, I will protect myself and this unit. And I will throw you to the wolves. Okay?

Sounds exactly like Red John to me. He tolerates Janes games. He has protected Jane on numerous occasions, the season 2 finale for instance. And then he assures Jane that he is not afraid to get him killed if he crosses the line.

S1. E11.
Watch Minelli closely here in this episode, that is all.

S1. E16.
Minelli very smartly walks away from the bombs location, he also call Lisbon in time to get her and Jane away from the bomb when he realises they are close to the mini-van with the bomb strapped to the guy.

Also in Season 1, Virgil mentions something about visiting his sister in Hawaii whom is sick. Maybe this has something to do with Red Johns connections to women and to my knowledge, all of Red Johns female victims were sisters in a family. Excluding Boscos assistant.

I've rewatched every scene Virgil is in, I'm now 100% sure he is Red John. And I also think his cult/following/gang, whatever you want to call it. Is a HUGE one. Brett Stiles in my opinion is also great friends with Minelli/RJ. S2E02, he just walks into the CBI headquarters alone like he knows the place and isn't afraid to confront Jane or Hightower. He also tells Hightower not to push her luck, in a manner as if to say, this will all soon be heard by RJ and we know what he will do if he finds out someone who he works with, is being mistreated.

Well Patridge is an obvious person to accuse because of his voice and dislike for PJ and the latest episode make it possible to be kirkland I am going with Bertram. Patridge was creepy and "erked" PJ tis creepy personality and cowardness would offend Red John. Red John has to be someone who can manipulate not creep people out, That level of sophistication takes him out. Kirkland is too obvious Bruno Keller is a smart man wouldnt make it that easy. RJ is constantly ahead of the game with PJ and so it has to be someone inside the CBI. Bertram has always enjoyed Patrick as Red John does, he is fond of him even after the whole issue with Highytower. He also has the financial means and connections to be Red John. Further more in alot of the episodes he plays dumb as if Patrick is teaching him along the way, which makes him less obvious along the way. He also has the training and background to know how to kill being in law enforcement. He also was at the mall, which gave him a front row ticket to see Patrick think he killed Red John. This is something Red John would never aviod seeing first hand.

So after the last episode, we now know Jane has a suspect list of his own and some notes to go with it. And here it is! :

Brett Partridge
-CBI Forensics Department
-Totally MACABRE
-Handled RJ Cases

Ellis Mars
-Bumbling sort
-"PSYCHIC"
-Todd Johnson investigation

Dean Harken
-Agent
-Bio Tech facility
-Red Hair

Jason Cooper
-Second in command at Visualize. Stiles coup.

Walter Mashburn
-PLAYBOY!
-UNLIMITED $$
-Intrigued by murder

Vint Molinari
-CBI Missing persons
-Searched for Kristina F.
Made no progress

Virgil Minelli
-Old CBI BOSS
-Retired

DR. Towlen Morning
-Family Doctor
-Deceased?
-Early RJ victims

Osvaldo Ardiles
-D.A's office
-Road Block

After seeing this list, I now strongly believe Minelli is RJ. Reason why you say? Red Johns character changes through the show, almost as if he's looking for a new game to play. Virgil retires around the time Red Johns character changes. Also, when Alexa Shultz called him in the flashback episode and told him about Janes absence over that past year, she told him that he was in a mental asylum (motive and 'inspiration' to mess with him even more) and also that "Its good to have friends in the FBI". And we know RJ clearly has friends in the FBI.