I haven't got this totallly worked out, but I suspect Red John is, or was, Angela Ruskin Jane.  "Ruskin Jane" can be literally translated as "Red John" or at least "Red haired John."  The evidence others have pointed to that point to Patrick are very compelling.  It is not inconceivable in this show that Jane, who has his nap problem is intentionally blacking out or has pre-programmed himself to obey "Red John."  

I suspect that Red John may have been his wife, themselves as a duo, or a complete fabrication applied after the fact to a serial murderer.  He may have faked his wife and daughter's death and buried his own knowledge of it in order to protect them from a greater threat, or criminal charges.  The spectacle and publicity were designed to make certain that the world at large believe they are dead, and that some other person's bodies were substituted,   

Perhaps she was a serial killer and he could not face this, but could not turn her in?  I think it is more likely that Red John is something they came up with pre-pilot episode to fake her death, and in the meantime he is stalking the actual threat to his family, who are in hiding somwhere.