In no order my top 3 suspects are

Ray Haffner
Gale Bertam 
Sheriff Thomas McAllister

"He is Mar" Mar or Mor (as pronounced respectively in eastern and western dialects, from Syriac: ܡܪܝ, Mār(y), written with a silent final yodh) is a title of respect in Syriac, literally meaning 'my lord'.

It is too obvious that Stiles would be "my lord". It's almost cliche'. Haffner is a good choice. The puppet master from within. Stiles may be involved in someway, knowing or unknowing. I think Stiles may be really wanting to help find Red John. Haffner leaves and approaches Stiles to fund him so he can continue the pursuit and help Jane. Stiles and Jane will continue with their relationship. Stiles will eventually provide more insight to Jane, with information passed along by Haffner. Jane will feel maybe Stiles is his man.

Haffner the puppet master continues to pull strings.

 

"He is Mar" Mar or Mor (as pronounced respectively in eastern and western dialects, from Syriac: ܡܪܝ, Mār(y), written with a silent final yodh) is a title of respect in Syriac, literally meaning 'my lord'.

It is too obvious that Stiles would "my lord". It's almost cliche'. Haffner is a good choice. The puppet master from within. Stiles may be involved in someway, knowing or unknowing. I think Stiles may be really wanting to help find Red John. Haffner leaves and approaches Stiles to fund him so he can continue the pursuit and help Jane. Stiles and Jane will continue with their relationship. Stiles will eventually provide more insight to Jane, with information passed along by Haffner. Jane will feel maybe Stiles is his man.

Haffner the puppet master continues to pull strings.

 

Some Fresh Perspectives You Might Enjoy:

1. Jane and Red John's handshake

The show included the scene where Jane first met Reede Smith and Thomas McAllister. The funny thing is Jane never shook hands with these two. It might sound like a trivial point but the shaking hand part is apparently of great importance to Jane, you might remember when Lisbon told Jane "... you met Red John ...", Jane interrupted her and said "not just met but shook hands". We first saw Partridge in the first episode of the show, he didn't shake hands with Jane either. One can argue they could've met before and shook hands back then, but my guess is the scene where the two shake hands is a crucial part which is definitely somewhere in the show. I'm not sure about Stiles, I just checked his first scene with Jane, they didn't shake hands. I think it's the first time Jane and Red John met that matters the most, the way Lorelei put it suggest this thesis. She said "I wonder why the two of you didn't become lifelong friends the moment you shook hands", She's implicitly referring to Jane and Red John's first meeting.

I distinctly remember Jane shaking hands with Haffner, Bertram, and of course Kirkland the first time he met these three. I'm happy with this, these three are on the top of my list, with Haffner being the #1 suspect, Bertram #2, and Kirkland #3.

2. Kirland: if not Red John then who?!

Kirkland is an interesting character regardless of him being Red John or not. A simple analysis might help us shed some light on who he really is. Jason Lennon claimed he gave Lorelei's sister to Red John, does that mean he necessarily knows Red John? He could've delivered her through a proxy or perhaps a Red John accomplice claiming to be Red John. One thing we can be sure of is that Lennon was a lead. Kirkland killed him after asking only one question "do you know who I am?", Lennon didn't, Kirkland looked like he was relieved from a heavy burden. Kirkland never asked about Red John or anything that might lead him to Red John. Since Red John's identity is something no one would refuse to know, from this we can rightfully infer Kirkland knows Red John. Moreover he's hindered the progress of the Red John case by killing a witness. This narrows down the available choices regarding Kirkland's role to three possibilities:

1. Kirkland is Red John.
2. Kirkland is Red John's loyal accomplice.
3. Kirkland is after Red John and he knows who Red John is.

Other established facts:
- Kirkland is interested in Jane's progress in the Red John case.
- Kirkland has the wrong list of suspects.
- Bruno Heller insists that one of the names on Jane's list is indeed his serial-killing nemesis. Follow this link to make sure there's no equivocation as some people would like to suggest. (source:http://www.tvguide.com/news/mentalist-finale-red-john-revealed-1064951.aspx)

It follows from this that Red John has the real list, therefore Kirkland is not Red John. So the first possibility is ruled out. And since a loyal accomplice would inform Red John of the list of suspects, and Kirkland didn't do so we can rule out the second possibility as well. The second possibility rules out "a loyal accomplice", not an accomplice! Kirkland could be a former accomplice or an ambitious cop, each of which is included by the third possibility. My guess, Red John's going to kill Kirkland.

Brett and Ray both belong to Brett's cult....I think when RJ started killing it was the younger Brett and then Ray his son took over once Brett got him trained. Ray and Patrick have chemistry and Lorilei said" I'm just surprised you were'nt best friends the minute you shook hands" Rj has a following just like Brett has and quite a large one at that. So my guess is Ray Haffner is related to Brett be it son or otherwise; and he became RJ once Brett got too high in his cult or too old.

Jane and RJ is just like Gibbs with Hernandez in NCIS.

Hernandez murdered Gibbs family so Gibbs killed him, Abbey and the rest of the team, including the director ! found out that he killed him and THEY WERE OK WITH IT AS THEY KNEW HERNANDEZ HAD MURDERED GIBBS WIFE AND DAUGHTER.

RJ didn't just cause a car crash that killed janes family he butchered an 8 year old girl and her mother.
Seriously what is Lisbons problem with jane killing the man who slaughtered his family ?

I really hope that they don't pull what happens on every show where they find out who RJ is and there's no evidence linking him to any of the killings ect.

I hope that jane finds him about to kill Lisbon and they confront each other, fight and Janes kills him.