Because the Red John Story is practically the entire plot of the series, the identity of Red John will not be revealed until the very end. So, all we know for now is who Red John is not.

1) Red John is NOT Alex Jane (Patrick's father). In Red John's note to Patrick, he accuses him of being a "dirty money-grubbing fraud" and a "dishonest little worm". In the episode Throwing Fire, we learn that it was Alex Jane himself who made his son a dirty money-grubbing fraud.