I believe red john is Virgil Minelli for a couple of reasons.
First, when Virgil gives Patrick Laroche's suspect list(or so he claims ),
of Red John's connection, he says it was through mysterious and underground methods. Secondly, as Virgil talks on the phone with FBI director Alexa Schultz, she mentions how good it is to have a friend in the FBI,
the same statement that Red John mentions to Jane from the backseat of the limo. I think Virgil is the man.
