OK, I've got a sort of theory going on although it's very flawed as it hasn't appeared in every episode... mine's along the lines of the Doctor (and maybe Donna) being revered as a God...
Obviously we sweep aside the Adipose episode...
Pompeii... they became House Gods
The Ood... the song of the Doctor will be passed on down the generations and every Ood will know of him and what he did
The Sontaran eps... I'm not too sure about, there was something in there but I can't bring it to mind right now
Then the Doctor's Daughter ep... again something there with him cracking open the Terraforma (sp?) effectively ending the otherwise seemingly neverending war and creating a whole new alliance and lovely looking planet therefore - theoretically - making him the creator...
Like I said, crackpot but thought I'd put it out there...
xx