Near the end of the episode, John is giving a speech After he returns with Charlie and Eko, the camera shows a shot of Desmond by the water, looking like Jesus.
In comparison to the Synoptic Gospels of the New Testament, John from Lost could be equated to 'John the Baptist/Prophet/Savior' who baptized Jesus. Desmond is seen by the water in another shot (which could be symbolic of Baptism) once again reiterating this biblical connection.
But this goes against the leading theory on the net which states that Johns speech was just a fulfillment of something said earlier by Desmond, as indicated by The Deja-Vu that Hurley experiences.
I have not looked any further into this, and I'm sure there are so many other theories it's not worth debating any longer. But this is what it reminded me of.