He definitely is red John. If you recall the lines red John whispered to Jane when he was tied to a chair and red John had to come and rescue him from the killers..he quoted a few lines by William Blake. And after an interview Bertram too quotes a line from William blake's work to Lisbon. Dunno if it's connection enough to deduce that Bertram is red John. And obviously the other things too fall in place like the fact that he is in CBI and he also is a plausible suspect in burning Todd alive. He was near the room. And another time when red johns lover (alleged) was poisoned they show a robust and huge guy coming from opposite direction in a view that was shot from behind the guy..that definitely makes it plausible that Bertram is the guy.

Most likely,Red John is a person Patrick Jane knows but is not aware of his dark side.It is probably an important person who can watch what Patrick and the CBI team are up to at any time.His IQ is very high,as he can manipulate people and make them do anything to please his desire.It is possible that Red John is a member of the team or a person who closely works with the team because of his apparently perfect knowledge about Patrick and CBI movements,as he is always one step forward.I cannot name a person but it is probably and important one in the show. I chose Gale Bertram just because i had to in order to post my theory.

I think that Gale Bertram is Red John.

In Season 3 Episode 16 where Hightower is thought to be guilty of todd Johnsons murder, Gale Bertram qoutes a William Blake poem.
The poem that Red John says to Jane in the season finale of Season 2 ,Tiger Tiger..., is also a william blake poem.

?????

Before Bertram is exonerated from the charge of being the mole he meets Lisbon in his office (without Jane, take note); look this images:
http://i48.tinypic.com/2a681va.jpg
http://i49.tinypic.com/2pu0k0i.jpg
http://i48.tinypic.com/1zezj8i.jpg
After Jane says that Bertram isn't involved with Red John. It's not a mole.
Timothy Carter must pretend to be him RJ. And he's believed RJ untile 4x01's end.
But there's a strange link to Bertram visible only after several visions of the episode:

http://i46.tinypic.com/2iaadlc.jpg

Why Carter reads (probably) a newspaper of previous day? The same of Bertram? Maybe in the news are writed the informations on Jane's family. And was made ​​to disappear and destroyed by Ron Deutsch, the security guard.
IN THE MENTALIST NOTHING IS PLACED AT RANDOM
When Gale Bertram says or does something suspicious, PJ is absent (poetry, tea, journal).

Following the logic: Bertram it's involved with RJ, in some way.
Is he a mole? I don't know. Is he Red John himself? Maybe. Certainly he's a strong suspect.

I like all your theories about Jane being red john, but has anyone else noticed that Director of CBI Gale Bertram has quoted William Blake several different times. Which red john is doing all the time too. He would fit the age range for red john better he was there just b4 Jane shot who we thought was red john at the end of season 3 then mysteriously no where around after he shots the guy and for there theory of red john possibly being a cop he would have to b high up in rank.