Spoiler:
Red John is Virgil Minelli (Gregory Itzin)

Virgil is in the series pilot, and is first introduced as Lisbon's boss, a career law enforcement agent. Virgil retires soon after. Virgil had been in his job at CBI for 8 years when he retires. Red John's "mistake" happened 9 years ago. Virgil has the contacts in his long career to allow for access to information to ongoing investigations. Virgil is able to find information that LaRouche is keeping secret showing that he still has current contacts and the willingness to skirt procedural and ethical issues to provide it to Jane.
He is never outsmarted by Jane in the manner that the rest of the CBI team seems to be.

Patrick Jane, Grace Van Pelt, Kimball Cho, Teresa Lisbon, and Wayne Rigsby: None of these can be RJ -- They all can be excluded because a RJ killing occurs while they are with someone else: you can't be in two places at once. Also, RJ can not be female: Recall the scene where Cho and Rigsby go to the convenience store to
find surveillance footage of a man buying a stuffed animal for Rosalind --a female would have been recognized right away, especially a tiny female -- RJ must be a male of somewhat average build.

In an interview, Bruno Heller tells us RJ is someone who has been in the series, and is a recognized actor (not a bit player). We are told this before any of the season 3+ characters are introduced, so it can't be the CBI director Gale Bertram, Hightower, or JJ LaRoche. The only other actor of great recognition introduced early in the series is Malcolm McDowell who plays Bret Stiles.

In Bruno Heller's original screenplay “The Network Draft”,  a character named "RJ Patel" is the CBI boss (renamed for the TV series "Virgil Minneli")  -- RJ, as in "Red John."

A lot of people feel that Virgil can't be RJ because of the episode where: Virgil takes the RJ case away from Lisbon and gives it to agent Sam Bosco.  RJ has Bosco's secretary, Rebecca, kill Bosco, which causes the RJ case to go back to Lisbon and Jane. If Virgil was RJ, why would he give the case to
Bosco, only to kill him a month later?  ...There are several reasons;
1. the investigation might have been going in a direction under Lisbon/Jane that caused RJ concern, so he pulled it away from them temporarily,
2. RJ could be testing Jane to see if he'd stick around with Lisbon and continue to solve crimes even if he was denied direct involvement in the RJ case,
3. thinking the FBI would might soon take over the investigation (or knowing that he was soon to retire), Virgil gives the case to Bosco to throughly (and selfishly) check to make sure his whole crime history is perfect. Rebecca is his inside spy.

Hi everybody,

Back in 2010, I started a web blog about Red John's ID which I unfortunately took it down due to time restrain. At that time, I was accusing Bret Partridge, the Forensic Tech as Red John based on the following theory:

In the episode where Bosco and his team got dispatched, Red John asked Rebecca to finish off the team she is working with. When Teresa took over the case, she urged Van Pelt and Rigsby to check out the surveillance cameras. At a certain moment, you could see Rebecca walking up the stairs with a tray of coffee, followed by a mystery man (which I credited him as "The Mystery Man" in my blog") That man was wearing the typical garments worn by Forensic Techs, windbreaker with FORENSIC lettering at the back...

hi im taylor. my theory is more like a fact. 
bret patridge is red john. evidence you say? well, in an episode jane was captured by some idiots and tied him up to a chair attempting to kill him acting like red john. and red john knew this was comming and he killed the people and ended up saving jane. he spoke to jane earlier in person but as his normal self. patrick jane didnt suspect a thing from him. but his voice gave EVERYTHING away!! i love this show. and there is proof on you tube. go tis url. 
http://www.youtube.com/watch?v=u1F2GdLLoWA watch before you judge! and comment what u think about this :)

Jane's father. I believe he is Red John. And his assistant within the CBI is Agent Ron. My theory is very simple:The smile smiling rather is based on Jane because his father felt betrayed and abandoned him when he left. How circence could kill and leave town without ever being connected to crimes. He use mind manipulation techniques would not be surprised, after seeing Jane doing this for years. Learned from it.The implicancia with Jane demonstrates personal involvement. See who abandoned the child on television causing it sparked his desire to kill. And keep pestering him every day. It is possible that he has joined the more people over the years or not. Everyone can find something great he is, when it is actually mediocre.Another clue is that Bruno Heller said that Red John has appeared in the series.Another clue is that BH said in an interview that the actor who plays him is famous worldwide. Let me explain: the actor who played the father of Jane attended the X-Files series and this series spun the world into a roaring success. And he played a serial killer in comentadissimo season. Nick Chinlund played the serial killer Donald Pfaster, killer of women. That is a killer was full of rituals that took just women.Coicidencia? Maybe. But I vote the father of Patrick Jane!

I’m from Uruguay and my English is not very good but I’ll try: Since season 1, the character’s development of Van Pelt seemed suspicious to me. I don’t think she is Red John because I believe he’s a man and older than Grace. But RJ could be someone related to her…
Reasons:
Just in the first episode of the series there are a lot of hints about Van Pelt but attention was directed only to creeps Brett Partridge and Dr Wagner.
- Van Pelt is the only one in the team who for sure arrives after Patrick. She’s the new one.
- Those gestures she makes when she wants to look like a good and sweet school girl. At the beginning seemed hers but now she uses them when she wants to manipulate someone. 
- How her face changes when she gets angry with Jane. Her comments telling him: Poor sad man, etc. Jane told RJ “sad, sad man”.
- Her dogmatic beliefs in psychics (cousin Yolanda), Red John wrote to Jane: “If you were a real psychic…”, he also believes in them.
-The comment Jane made to Wagner: Why magicians have beautiful assistants? To distract attention! Van Pelt is red haired and beautiful. She’s distracting everyone.
-How could Jane know her father was football coach just from her demeanor? Suspicious… maybe he knows her, recognizes her. Also, Jane told her she believes in Yolanda because she let her talk with someone who died and VPelt loves. (Her sister who committed suicide…, maybe because of Jane?)
Well, now I have to go but i'll come back with more reasons.