http://www.zen134237.zen.co.uk/Mentalist/The_Mentalist_1x01_-_Pilot.pdf

That's a link to the original script for the very first episode! The CBI boss is called RJ! Explains it all really.

S3. E10.

Patrick approaches Minelli (Minelli refers to PJ as just Patrick, like Red John does) while fishing and tells him he has the upper hand on Red John. Minelli laughs and says to Jane "You sound nuts my friend". At the end of the episode, we also learn that Minelli has stole LaRoches suspect list to give to Jane.

Virgil Minelli: LaRoche's suspect list. Secured through back channels, and personal favors. LaRoche has no idea I have it.

Sounds like something RJ would do, doesn't it?

S1. E04.
Virgil Minelli: Jane, you close cases. You - you close like a fiend. So I tolerate you and I - I protect you. And I let you make Lisbon's life a misery. But there's - there is -there is a line. And when you cross it, I will protect myself and this unit. And I will throw you to the wolves. Okay?

Sounds exactly like Red John to me. He tolerates Janes games. He has protected Jane on numerous occasions, the season 2 finale for instance. And then he assures Jane that he is not afraid to get him killed if he crosses the line.

S1. E11.
Watch Minelli closely here in this episode, that is all.

S1. E16.
Minelli very smartly walks away from the bombs location, he also call Lisbon in time to get her and Jane away from the bomb when he realises they are close to the mini-van with the bomb strapped to the guy.

Also in Season 1, Virgil mentions something about visiting his sister in Hawaii whom is sick. Maybe this has something to do with Red Johns connections to women and to my knowledge, all of Red Johns female victims were sisters in a family. Excluding Boscos assistant.

I've rewatched every scene Virgil is in, I'm now 100% sure he is Red John. And I also think his cult/following/gang, whatever you want to call it. Is a HUGE one. Brett Stiles in my opinion is also great friends with Minelli/RJ. S2E02, he just walks into the CBI headquarters alone like he knows the place and isn't afraid to confront Jane or Hightower. He also tells Hightower not to push her luck, in a manner as if to say, this will all soon be heard by RJ and we know what he will do if he finds out someone who he works with, is being mistreated.