I think we may have been given another clue about Red John during the final 10 minutes of the show.  Lisbon was looking at a computer display with a map of California and each of the cell phones she had tapped (P-Partridge, B-Bertram, H- Hafner, M-McCallister, K-Kirkland, and S1 and S2 for Smith and Styles).

If we the map was correct and each of the suspects actually had their cell phones, then we can probably rule out a few folks.  Kirkland was in LA, and Styles and Smith were both in the San Francisco area.  Even McCallister appeared to be about 45 minutes away from the house where Partridge was killed.  The two suspects who appeared to be near the home were Bertram and Hafner.

Since the show went out of it's way to point the finger at Bertram, I think Hafner was the one most likely to be at the house ... if it was, in fact, Red John and not one of his accomplices.

Heres an interview with heller that happened after the premier http://insidetv.ew.com/2013/09/30/the-mentalist-season-6-premiere-post-mortem/

PEOPLE, HAVENT YOU SEEN THE HIDDEN CLUE HELLER HAS TALKED ABOUT, ITS OBVIOUS, REALLY OBVIOUS THAT CBI RON IS WORKING FOR RED JOHN, HE APPEARED AT THE VERY END OF THE EPISODE, HELLER SAID IN THE INTERVIEW THERE IS GOING TO BE A HIDDEN CLUE AT ALL THE LAST EPISOODES, IT WAS CLEARLY OBVIOUS THAT PARTRIDGE WASNT RED JOHN AND HE WAS AN INNOCENT AND CREEPY GUY,

I THINK RAYMOND HAFFNER IS THE ONE , BERTRAM ISN OW TOO OBVIOUS, KIRKLAND IS ALSO WORKING FOR HIM, WE SAW THEM CHATTING IN A SCENE IN SEASON 5 ... THEY ARE BOTH WITH RED JOHN, MCALLISTER AND SMITH DOESNTHAVE ANY ARGUMENTS TO BE RED JOHN, AND STILES IS RED JOHNS FATHER!!

I think its haffner

My personal theory is that Red John is one step ahead of Jane because he has people in every law enforcement division (local, state, or federal), not because he has "psychic powers" or whatever it was Mr. Barlow was getting at in the season 5 finale. 
Gale Bertram - CBIThomas McAllister - Napa CountyReede Smith - FBIBob Kirkland - Homeland Security
All of the above are likely moles for Red John who work to keep a surveillance on Jane. This leaves Brett Stiles, Brett Patridge, and Raymond Haffner. Before I get to them, I want to include the possibility of a fifth mole who works for Red John. If RJ is always one step ahead of Jane, then what if he had a mole in Lisbon's team all along. The likely candidate for this would be Grace Van Pelt because she was a late addition to the team. As a matter of fact, she was only considered after Jane became a consultant, thereby causing one person in Lisbon's team to move to another division. Red John has no magic powers. He simply has the resources to influence people who work for the law, something Jane doesn't have. 
As for the three, I will rule out Brett Partridge for the following reason: He and Gale Bertram are the only ones appearing in the season premiere. If the list will be reduced to six after the first episode, then Partridge will likely be eliminated because Bertram appears in the next few episodes. This leaves Stiles and Haffner. What do these two have in common? Visualize. 
I personally think it's Ray Haffner because he fits all the criteria. If these two are the only ones left then things can go in many ways. It could be that Red John, as a member of visualize, carried out his acts of murder alone or with the help of Stiles' cult (or Stiles himself). It's a game of chess. RJ's subordinates who died carrying out his orders were the pawns and the suspects who work for law enforcement were his rooks, bishops, and knights. Stiles and Haffner are the king and queen, figuratively speaking. 

I feel sorry for those who still think Patrick is Red John, you guys really need to see a doctor! Simon Baker and Bruno Heller have both said Patrick is not Red John, and Red John is someone on the list, and he is a person, not an organization. It's not Mashburn, Lisbon, Van Pelt, Jane's father, or Cho! Grow up please!

With all due respect guys, some theories are as stupid and ignorant as it can get. Please think a minute before you post a theory and respect the readers. Please know most who come here are fans and know enough to see how nonsensical your claims are. At this point claiming Patrick is Red John is a direct insult to visitors of this website.

This is a longshot but I watched and listened to Lorelei read the
list over and over.  While she read most of the names on the list with a certain rhythm, she
hesitated slightly while reading Haffner's name.  I feel this may have
been her attempt to give Patrick one final clue before Red John ended
her life.  Don't know, but I am sure anxious to find out!

Who's excited http://www.spoilertv.com/2013/09/the-mentalist-season-6-red-john-final.html