I believe Patrick Jane is Red John.

If we put aside the obvious and blatant connection between the names "Jane" and "John" we should consider the conversation between Jane and Tommy in the episode "Red Flame" about "Moby Dick": Tommy states that the whale died at the end. Moby Dick killed Ahab, but survived. That story, like the Mentalist tells of an endless hunt that ultimately destroy's captain Ahab. Keeping PJ's promise that when he finds RJ he will kill him (and thus revealing the anger in him) tells of an upcoming showdown which the "psychic" RJ should be able to prevent just by killing Patrick in the same way narrowed the suspect list despite that "nobody" knew of the said list.

Another evidence of this connection is the fact that Red left agent Lisbon alive when he so easily could've killed the person that matters the most to Jane just as he did in the pilot.