1 - He is well-known for being an expert in Electronic surveillance.
Now... it is clear that Red John has been listening to the team's phone calls and has traced their positions all the time (unless he has psychic powers, which we know he hasn't -- the Mentalist is not Lost).
He has always been one step forward, and there is evidence that he knew new information as soon as the team members knew it (because he killed many witnesses at the very last minute - if he knew "everything" well before Jane & Co, why he didn't do the job well in advance?)
He killed Dr. Miller after Patrick left a message on her voice mailbox.
He reached the place where the three copycats were keeping Jane prisoner just a few hours after Jane left a message for Lisbon in which he said he was getting closer to the killers.
....and many other cases.
We've seen Van Pelt bugging and tracing the suspects' phones. Why shouldn't a former CBI agent, EXPERT in electronic surveillance be able to do that?

2 - His name is only a vowel away from one of his aliases: Ray ..... Roy (Tagliaferro)

3 - He is one of the three suspects whose age is consistent with being "some kid" at the Visualize farm in the late 80s when a young RJ painted the red face on the barn. Stiles, Bertram, McAllister are too old to be called "kid" 23-25 years ago.
This leaves us with only Haffner, Smith, and Kirkland. Among them, only Haffner is a known member of Visualize.

Why doesn't Jane just put the suspects in front of that blind woman who knew Red John. She could tell Jane which one is the man she knew. They could also narrow it down by getting alibis from the suspects for the time during which Red John was painting Lisbon with blood. I'm sure that would narrow it down considerably. You know, old fashion police work and all. There is no way all of the suspects are without alibis for all of the Red John killings. This whole storyline is a farce. You could drive a truck through the holes in the Red John plot.  Thank goodness they're wrapping this up soon! 

Theories are based off memory and the belief that the list holds true.

Let’s begin by eliminating two suspects:

Brett Partridge
He was murdered by Red John and confirmed by Bruno Heller in an interview
to be dead.


However, this leaves us with two major questions.

1) Why was he killed?

I’d prefer to think of it as Heller killing him rather than Red John killing
him. Partridge was the number one suspect for a majority of people, such a plot twist
would leave us scrambling to reason out a new favourite suspect and it makes
for a more thrilling story.

2) Why did he say ‘tyger, tyger’?

He was hypnotized by Red John and Lisbon opening the door was the trigger (I believe
RJ also hypnotized Kristina Frye into thinking she is dead), he promised to say
it to avoid further torture and the third reason I’ll explain further down.

 
Bob Kirkland

He had homeland security agents break into Jane’s room to steal information on
RJ. This occurred several episodes after Lorelei was found murdered therefore
RJ knew who the 7 suspects PJ would narrow down to very early on.


Remaining questions:  Why does he want to
be kept in the loop on the RJ case? Why did he steal PJ’s info? Why did he
murder Jason Lennon and asked do you recognize me before doing so?

My theory is that he, like Patrick Jane, is looking for revenge. I believe RJ
murdered Kirkland’s family decades ago while he was in the house, most likely
hiding and at some point made eye contact with Lennon. But unlike PJ he isn’t smart
enough to figure it out on his own. To further my theory on Kirkland, I think
Heller + writers made him a homeland security agent to mean protector of his
home (to make up for something he couldn’t do when he was younger when RJ
murdered his family). And the synopsis for season 6 episode 4 reads: Jane
reveals that a list of fake RJ suspects he planted was stolen and the team
realizes these men are in danger.

Assuming
Rosalind Harker’s description of RJ is reliable we can quickly eliminate three
more suspects
Bertram: too bald
Stiles: too old
Smith: too chubby


Leaving…
Haffner: Visualize connection, more
physically capable
McAllister:
still a mystery so good writing potential, has a more mature/leader-like look

Both of whom were whistling in episode 2.
But
I’m sure these two suspects are exactly who Heller wants the audience to
have as their number one picks before pulling another twist. We are merely
puppets to him.


A popular theory is that more than one of the suspects is ‘RJ’. For my version
of the theory I think Bertram, Stiles, Smith, Haffner, McAllister and even
Partridge are RJ. Partridge was the one who saved PJ from the copycat murderers
which explains his connection to “The Tyger”. He sacrificed himself to ensure
the survival of RJ by attempting to throw off PJ. Bertram, Smith, Haffner and
McAllister can all manipulate law enforcers, investigations and evidence (three
of whom we see suspiciously chattin’ it up in episode 2) and Stiles is the
recruiter for disciples. So perhaps Jared Renfrew was trying to write ‘He is
many’ before he died.  However, this
theory is somewhat anticlimactic so I prefer the RJ is just one person theory.

I still think it is Haffner, on probability, but check out the Canadian promo for next week's episode:

http://www.spoilertv.com/2013/10/the-mentalist-episode-603-wedding-in_6991.html

"He is an excellent whistler" Dr.Sophie Miller

Ray Haffner = Red John

Reasons

1. In episode 13 season 4 Red is the New Black RJ literally shows his hand. When you compare (color, shape and size) the hand with remaining suspects the most likely RJ is Ray Haffner. 

2. He is visualize and his age would suspect he was young enough to be at the Visualize barn.

3. He's got something in common (not only appearance) with PJ and that is his love for Lisbon

I believe Red John is Ray Haffner on multiple cases. First Haffner appears in the episode the Little Red Book which happens right after Jane gets out of jail from killing Timothy Carter (Red John Imposter) making Jane a little distressed and hurting his focus. The episode placement is perfect since everyone thought Jane killed Red John but since he did not people will think that Red John will not be seen for several more episodes except they slip in Haffner who the audience is not concerned about since Red John is not dead. Also Haffner fits the description of Red John and falls into Jane's trap in the Little Red Book episode making himself look weak compared to Jane. Another reason why Haffner is Red John is because he likes Lisbon which explains why Lisbon was not harmed when Red John took her. Haffner is also known to be a good wiretapper and surveillance expert which shows how Red John is always in Jane's head while Jane is more person to person and lacking in technological skills. Haffner could also be Red John since in Black Winged Redbird the person who visited Sophie Miller ( Jane's psychiatrist) was named Jay Roth. If you changed the J to an R it would be Ray Roth or Red Ray since Roth means red. In addition to everything Haffner has appeared in episodes only with the word Red in the title and is a Former FBI Agent and CBI Supervisory Specialist and currently a private detective and member of Visualize showing that he has strong connections with all of the agencies.