I would put my money on Bertram as RJ. 

In the episode "Strawberries & Cream part 2" Bertram had been given the room number above O'Laughlin in the hotel, where Hightower was purported to be staying. That is the room that the assassin first enters.  Why would RJ's assassin bring tools to repel to the room below rather than simply enter the correct room? One possibility is that both RJ and RJ's accomplice (O'Laughlin) had been given different room numbers and RJ did not know which was correct. Thus, the assassin needed to bring tools to access both rooms.

In the same episode, Bertram (inadvertently?) gives Jane the idea that the assassin's rope is an important clue by stating that Jane appears to be at the end of his "rope." This is what changes Jane's opinion that Rj's accomplice is O'Laughlin, not Bertram.

Finally, Bertram can use his position at CBI to facilitate the hire of his associates within the agency and arrange for the elimination or transfer/escape of those in  CBI custody who might know his identity.

No-one liked o'laughlin very much. He seemed annoying and everyone hated how he "stole" van pelt from rigsby. So what does bruno heller do? He makes o'laughlin the fbi mole who gets killed at the end of season 3, much to everyone's delight.

So with that in mind, you can see why bertram has to be red john. He is for sure the most annoying character now that o'laughlin has gone. Type in "gale bertram" into youtube and click on the second option "forget about jane". Gale bertram is red john because:

1) He is annoying, so it will be a satisfying finish for the audience if he was red john and killed by jane at the end of the series.
2) He is powerful, being the cbi director.
3) Although he doesn't fit the description of red john by rosalind harker, the man she was describing was likely an accomplice, a profile bruno heller used to throw us off from the real red john - bertram.
4) He both hates and admires jane at the same time, which fits the character of red john.
5) I am usually successful at making predictions with crime shows, so if i say red john is gale bertram then he probably is red john.

I think that Red John is Gale Bertram because:

-He has shook Jane's hand(3x01)
-He drinks tea(3x24)
-He quotes part of the William Blake poem(3x16)
-He helps to frame Hightower when he informs La Roche that Hightower had a relationship with one of Todd Johnsons victims which shows she has motive
-He hates Jane and was disappointed when Jane didn't go to prison for killing Timothy Carter
-He is quite powerful because he is the CBI director
-When he first meets Jane he calls him boy wonder which is what Jane's father called him and not many people know that.
-Jane said Red John would be at the mall on the season 3 finale and he wouldn't have been talking about someone like Timothy Carter maybe Red John was there which would mean Bertram.
-A lot of Red Johns friends are from the police which is people that Bertram can get to help him
-Bertram led Jane to O'Laughlin by mentioning Rope and O'Laughlin led Jane to Timothy Carter who Jane killed and went to prison for it.All caused by Bertram and to do that he had to know that Jane was setting a trap for the CBI mole because O'Laughlin told RJ and if RJ is Bertram thats how he would have found out.

   We may have been looking at Bertram to be the CBI mole and the whole
   time he could be Red John.
 

Leave in peace: Alex Jane, Patrick Jane, J.J. Laroche, Kristina Frye, Robert Kirkland, the CBI team and all the people not mentioned in the list.

Brett Partridge
Yes he surely fits the description. But you have to enter into the season mind. Think of it: it's a duel of the mind, a duel of charismatic and sofisticate individuals. Partridge seems to me just a guy friend of RedJohn because RedJohn let him do the dirty jobs Partridge dreams about.
Supporting this Partridge is the real RJ mole in the CBI. More other thing, in the season 3 finale they won't find out the CBI mole, they only find out that O'laughling (the hell is written that name?) is RJ's friend so the mole is still working for RJ. Obviously is Partridge in the season 2 finale and I believe that's him who makes the kills when the real RJ could not so the real RJ as got a pretty damn good alibi.

Ellis Mars
"He is Mar" He is Mars?
Surely Mars is an intriguing character. You will never bet he is RJ so maybe it could give the writers the perfect twist ending. You didn't see it coming do you? Till the very end ah? It fits the show. But yet i'm not convinced.
If he is RJ then he deliberated play the role of the idiot just to meet PJ. Well you can say that when Mars wanted Jane to treat him seriously simply said to him "You are a sad man, full of pain" "I can see it in your eyes".


In the list there is a priority in order of suspects. If they were only 3 we would have already known who RJ is so some of them are put in there just to make quantity. These are:

-Oscar Ardiles
-Vint Molinari
-Dr. Towlen Morning
-Dr. Linus Wagner
-Jason Cooper

Another reason they are in there is because Jane will investigate them all so he will not get immediatly new clues and the show will go on.
He wil investigate alternating a real suspect (for example Partridge) with a less probable one (Linus Wagner).

Dean Harker
Lisbon said "CDCA is powerfull, plenty of politicians friends and rich" so if Dean is RJ then he knows the right people. Has the resources.
But there is something wrong with this guy. The hairs. RedJohn isn't RJ because of the colours of his hairs.
From what we know RedJohns lovers all had RedHair. He pictures the face with blood and paints the nails with blood. He is obsessed with colour red. Harken simply fits way too much to be RJ. That's the problem. Where is the twist? So instead, let's give them a bunch of clearly fake RJ a too much probable RJ so they really won't figure out who RJ is! Let's play with their minds.

Walter Mashburn
Yes he is rich, powerfull, handsome, a latin lover. Plenty of resources, plays with Jane and likes him very much. They could be best friends in my opinion but Lorelei said "i wonder why you two didn't become best friends the very moment you shoke hands" so they aren't friends!
They dislike each other regardless of their similarities.
Mashburn is not.

Virgil Minelli
Minelle doesn't dislike Jane. He helps him out even when he doesn't really want to. He is way to old. He has done his part in the story and now he is out.

And now I will tell you who RedJohn is.

RedJohn is Gale Bertram.


GALE BERTRAM
There are many things supporting this
-"He is married"? could be. 
-He drinks tea (season 3 ending, lisbon enters his office)
-Was reading the same newspaper Timothy Carter was reading the day after at the mall. (season 3 ending)
-When Jane told him that Hightower wants Bertram to be at the meeting he made a pause to think, then agrees and when PJ leaves the office the thing he does is to use the phone. Why? To set up the trap for Jane.
-He is the proper age.
-His CBI position grants him important politicians friends, such as a perfect cover up for his real nature. Who would accuse the head of the CBI? Really who?
-He doesn't like Jane. He fights every time he and Jane are in the same room.
-Wanted Lorelei in the custody of the CBI at any cost.
-When in the mall with PJ told him the thing of the rope (just when he started to realize the real meaning of his presence) just to create a reason to leave the area.

Then ho please come one Kirkland? Why? Please make a list like I did for Bertram. When you got it with the same clues then come here and say that it's unreasonable! : )

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.

If I were a betting man, I would place my money on Bertram.

I'd also place a wee wager on either Stiles or LaRoche!!

According to me the characters who fit better RJ's personality are
-Stiles: maybe too obvious
-Mashburn: but I'm not sure he fits RJ's physically description
_Bertram: He was my first suspect, why did he quote the same Blake's poem of RJ? it can't be a coincidence. Being so self-confident and making the challenge more interesting is typical of RJ.

Before I saw Red Sails in the sunset I had thought that Mr. Volker could have been a suspect too. He's rich, powerful, very self confident. But Lorelai let me think that PJ knew RJ's alias since pretty log time.
So kirkland wouldn't be a suspect too. Anyway I think Volker will come back soon, He's a too mysterious characters to leave him to gather dust.

About the other suspects, they don't convince me too much, surely some of them are involved (I'm sure GVP is already to RJ's side, I mean there's some dark in her) but they can't be RJ