Right now my top suspect is Ellis Mars aka Lamar Ellis

In Season 2 Episode 2 (I think), Jane has a conversation with Bosco in which they play on the phrase "Cover Up" and as Jane is leaving Bosco drops the file in a basket covering up another file that read:
Superior Court - LA County
   Statements - Case# 42-53-2A
Attn: Lamar Ellis

Then in a later episode we meet a man calling himself Ellis Mars pretending to be a psychic.  He acts a bit goofy to throw everyone off but he correctly predicts there will be another murder.  Then when Jane has Mars in the hotel room and the killer, a Red John accomplice, comes in the Killer says to Jane "It would blow your mind" in reference to who Red John is.  That Jane had Red John (Ellis Mars) right there in the room would blow his mind. 

My #2 suspect is Bertram and his assistant.  This works for many reasons already stated in others theories.

In Reality I doubt that Bruno Heller has decided exactly who will be Red John.  He has left things open enough that it could plausibly be 10-20 different characters.  Also with Red John using so many accomplices any one who appears a solid suspect could be written as just another accomplice.