Partridge in my opinion is unlikely. Jane reads him like a book when they first meet, but yet struggles to figure out RJ. Jane instantly realises this man is physically turned on by murder which could be a plausible reason to be RJ. Lets not forget Red John has friends, a man of Partridges character is far from like-able or friendly. He is also too young.

Mashburn, well over 6ft tall. Has the power, fame and charm to sleep with a vast number of women so why sleep with Rosalind? I think the chances of him being Red John are really slim.

Brett Stiles. A man with mentalist power, connections in law enforcement, an intellect comparable to Red John and also not afraid to kill people/get them killed. BUT. Red John has a ritual, where as a murder Stiles is guilty for was nothing like Red Johns MO. Brett Stiles is also a very identifiable person, Rosalind would have mentioned Roy was very old, spoke very posh and is losing a considerable amount of hair.

Minelli. Joined the CBI soon after Red Johns mistake. Very like-able person, seems very soft and lovable. Loves to drink tea/coffee. He's the only other person in the whole of CBI other than Bosco and his team to know about the body with Red Johns mistake. He quits after the evidence against Red John is destroyed. After he quits, Red Johns personality changes almost as if he's quit too and he's looking for a new game to play. Only someone of really high power in the CBI could access the files and send that video to Van Pelt. He's the only person who knew what Tagliaferro meant. He went away on vacation supposedly to see his sick sister, shortly after that we find out Red John has built this hideout. His concern for Rosalind is clear and the way he holds that stuffed elephant is almost as if it means something to him. He's under 6ft tall, not weak but not muscular. Called Jane nuts when he said he had the upper hand on Red John.

Surely Virgil is RJ, No?

Virgil Minelli is an Italian name. Tagliaferro is also an Italian name.

Google : Dante and Virgil at the gates of hell.
Don't be too surprised when you see who the illustrator is.

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.

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.

I often wonder how a serial killer have this much power over police forces and know political figures. the answer I came up with is that they don't know they work for RJ. So he have to have a powerful job, like being the head of CBI. I don't think red john is a simple guy working at CBI like Ron. He can't be jane or anyother main character, simply imposible for them to pull of something big as this(how would they have moles in fbi?). I am not sure who red john is but I wish, I helped you eliminate some of the options..

Did anyone else see the photo on Walters desk in the last ep??? I'm sure that was Virgil with walter or maybe I'm just seeing things, at the moment I'm hoping its either Minnelli or partridge, because to me they make the most sense.

1. It's not Patrick. (Yes, it is really not Patrick)
2. It's not his father (RJ did this because he was "slandered in the media").
3. It's not a woman. (it should be obvious, but for example: RJ slept with Rosalind and I don't think she's lesbian)
4. We have already seen him.
5. A powerful and influential person.

So I'm going for Virgil Minelli and my secret favourite is Bret Stilles

In the end the truth will come and set us free