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.
