I feel a little ridiculous posting a theory about Red John at this point, but in the spirit of a 7th season, technically, it's still possible, and I can't believe I'm gonna say this but...I think
Ray Haffner is Red John


There are SO many reasons why, and we all know the majority of them

Just wanted to add that I find the most compelling clue about Ray is that he is the ONLY character on the show who has a connection, and/or access and information to ALL of the organizations in question:

VISUALIZE, FBI, CBI, BLAKE ASSOCIATION



1.  VISUALIZE supposedly turned Ray's troubled youth around -- or maybe it actually unleashed his love of power and killing.  Ray's early time at Visualize coincides with Elliston Farm murders, thus it would be very easy for him to have been the killer.....where he painted his first smiley face.  Ray's also the right hand guy to Visualize power monger BRET STILES 

2.  Ray is a former FBI BOSS -- would be very easy for him to have "friends" in the FBI.  


3.  Ray specialized in TAKING DOWN ORGANIZED CRIME -- thus it would be very easy for him to know about and have a hatred for THE BLAKE ASSOCIATION wanting the organization to be exposed

3.  Ray became CBI BOSS right after fake RJ Timothy Carter's shooting, attempting to take over the CBI would conveniently give him future control of the Red John case -- until Jane gets the old team back -- but not before Haffner tells Jane that he'll pay for giving Haffner a hard time.


THUS:  RAY HAFFNER'S journey as RJ RED JOHN, in order, from the beginning of RJ to now, has gone like THIS:    VISUALIZE, FBI, BLAKE ASSOCIATION, CBI



And so far, Jane's hunt for Red John has taken him from: 

CBI, BLAKE ASSOCIATION, FBI and I predict for Season 7…..VISUALIZE 

THIS IS THE EXACT OPPOSITE OF RAY HAFFNER!!  Jane is working his way into the inner world of Red John!


SO, IT ALL BEGINS and ENDS with VISUALIZE!!  Visualize is where Ray became Red John, and Visualize is where Jane will catch Red John, AKA RAY HAFFNER, who is alive and well with Stiles hiding out


ALSO: Ray's an expert in wire tapping and "creative" surveillance -- and surveillance has been an ongoing theme on The Mentalist.  Surveillance is how Red John always stays two steps ahead of CBI team and Jane.
 


FUN FACT:  REED EDWARD DIAMOND's initials are RED