This is not really a theory, but have you noticed that after 6x08 " Red John" the episode titles are:

6x09 My blue (!) heaven
6x10 Green (!) thumb

Break of colour. Does that mean, that the "Red John Case" is finished after that? Does he die? What is your opinion?

Something new (sorry...).  This is more about how things developed rather than who Red John is.  I strongly want Red John's connection to Jane to go back to Jane's early days.  Such a connection would be more powerful drama than merely a serial killer annoyed by critical on-air comments by a minor entertainer 10 years ago.

What is Bret Stiles's back story, where did he come from?  Jane calls him just a con man.  If so, did he know Alex Jane -- maybe not a carny, but a con man acquaintance in the fluid world of non-violent criminality.  Both Stiles and Alex Jane would be in their mid-to-late 20's before Patrick Jane was born (40-plus years earlier).  

What if, with his ample charisma, Bret Stiles seduced Alex Jane's wife and is the biological father of Patrick Jane?  (Yes, this could be soap-opera lurid, but not necessarily.  Bear with me.)  Stiles would have no interest in actually raising a child, so I could see him content to let Alex be the putative father.  If Alex knew or suspected Stiles was the father,  Alex might have little love for Patrick and could readily exploit him in the show, especially once his wife/Patrick's mother was out of the picture.  (BTW, Patrick Jane seems unusally sensitive to people ill with cancer and is afraid of doctors and pain.  Did his mother die young of cancer?  I assume he had a positive relationship with his mother or he could have grown up to be a socio/psychopath if neither parent provided love or nurturing.)  As Patrick's intelligence and talent became apparent, Alex might come to see even more of Bret Stiles in his putative son, resenting him even more.

Meanwhile, Bret Stiles is founding and growing the Visualize organization.  Assume a seriously disturbed young adult (late teens, early 20's) joins Visualize--Ray Haffner, Brett Partridge?--25 years ago.  Visualize straightens him out to be functional (off drugs and alcohol).  Intelligent and talented, he becomes a protege of Bret Stiles, but Stiles can't eliminate his darker impulses.  (This would also work if Red John were another illegitimate son of Bret Stiles, but that would be way too many coincidences for any reasonable plot.)

The protege becomes Red John and first murdered at the Red Barn, perhaps triggered by drugs (speed) and sleep deprivation.  The Visualize farming attempt fails and the protege -- now off the speed and no longer sleep deprived -- pursues a career in law enforcement and crime as a crooked cop (remember Orville Tanner was a criminal as well as participating in the first recent Red John murder).  This could account for the 10+ year break in Red John-style murders.  Something -- don't know what --would then have triggered him to resume murdering.

This helps explain the following:
o  Jane is gifted with extraordinary intelligence and talents as Stiles's biological son, despite Alex Jane's mediocrity.
o  Knowing his paternity, Bret Stiles has affection for Patrick Jane which increases as Stiles recognizes similarities in Jane.  Stiles makes strangely personal commets to Jane in several episodes.
o  Stiles knows who Red John is and disapproves of the murders -- especially murders for the sake of killing (vs. for practical reasons such as eliminating a competitor, etc.).  But, having had a role in creating Red John, Stiles protects him to protect himself and Visualize.  It is possible Stiles occasionally uses Red John to murder to further Stiles's Visualize interests, too.
o  Initially, Stiles protects Jane from Red John's worst impulses.
o  Once Red John learns of Jane's link to Stiles, there is a tangled mix of jealousy and affection, especially as Red John develops a fondness for the cat-and-mouse game with a worthy opponent.  Red John ends up displacing his anger over the on-air comments by murdering Jane's family instead of Jane himself.  Ultimately, Red John has equal parts resentment and love for Jane (Heller's duality theme) and both torments Jane and protects him.  Jane is thus uniquely able to hunt Red John without immediately being killed by him.  Ultimately, Red John appreciates the irony of hurting Jane far more by keeping Jane alive than he would had he killed him, and, benefitting from the entertaining game between them.

Finally, this sets up the possibility of salvation for Jane.  It would mitigate Jane's guilt if Red John had his own reasons for killing Jane's family.  I think the Tyger Tyger law-enforcement organization is a competitor and threat to Visualize.  I hope and assume the law-enforcement corruption and Visualize provide the new long story arcs once Red John is wrapped up.  (Like others, I will be disappointed unless Red John is one person who can properly be the focus of Jane's revenge.  That doesn't rule out a group of Red John friends, but there must be one Red John heading it.)

This doesn't advance the "who is Red John" question, but it's fun to speculate.  BTW, I know others have already floated the idea that Red John is the son or protege of Bret Stiles.  I'm not trying to take credit for others' ideas.

Thanks for reading this.  Comments -- pro or con -- welcome.

It will definitely be Bret Stiles.  I can only offer meta proof, no actual proof.  For one, he is the biggest star on the list of characters, and as Family Guy said, it's always the biggest star.  For two, he is the only leader of a cult-like organization and a conspiracy of this magnitude will take a cult leader to inspire it all.

My theory will probably not be among the most popular theories here but here is how I see the things.
We all are aware that only people from the list of 7 were able to be on the right places in the right time for killings that Red John committed.
We are also aware that Heller already stated that "we can trust the list," but also that we would be disappointed when we find out who Red John is. We also heard that after some time in season 6, it will no longer be about who Red John is, but about catching him.
Therefore, I can state my theory here:

Red John doesn't exist as a single person. There might be a leader of the Tiger,tiger organization, but that's all what his job is. All of the Tiger, tiger members are actually Red Johns for themselves. The organization kills everyone who comes in their way somehow, and acts under the alias of Red John. It's simple, they have many regions covered, they act together, and share their assignments.

Sheriff Thomas McAllister is, for example, Red John for Napa county, Gale Bertram's job is to keep Patrick Jane in his sight, and under his control. We've seen Reede Smith in action in the last episode. Brett Partridge's job was removing the existence of  eventual evidence that was left on crime scene. Bret Stiles' job... probably the biggest one, he's most probably the brain behind this whole organization. Ray Haffner... well, you can call him Roy Tagliaferro if you preffer.
The thing is that the list is probably too small for everyone that is involved.

Also, remember the "He is man" clue from Mexico, in an opening season. Thinking about it now, "he is many" would fit perfectly.

I've kept it short and brief, so I probably left some things unexplained.