So, okay. Doctor Who?
Between The Big Bang and The Doctor's Wife, we've been working from the template of a guy who just stole his TARDIS because he wanted to go exploring. (One of my favorite moments in series history is in The War Games when the Doctor admits to Jamie and Zoe that he stole it, and when they incredulously ask why, he responds, "I was BORED!") But the McCoy era played up the idea that the Doctor was lying (hm, sounds like a phrase we've heard recently) and had a much less whimsical agenda. Remembrance of the Daleks throws in the retcon that the reason he was on Earth in the first place, back in the very beginning of the series, was to hide Time Lord artifact the Hand of Omega. (Oh hey, we've been seeing some omegas on the show, too!) He even hints in dialogue that he was there when it was made -- which would suggest he was actually far older and more important than had previously been implied, and indeed probably a founding Time Lord along with Omega and Rassilon.
io9's review of the finale links the TARDIS Wiki entry for
Cartmel Masterplan:
The overall plan for Cartmel was to reveal that the Doctor was some form of a reincarnation of The Other, a mysterious figure from Gallifrey's past who helped form the Time Lord society and perfect the time travel technology of the Time Lords.
So yeah, pretty much what I just said.
I suspect that's got something to do with where all this is going, the idea that the Doctor's very identity is some sort of horrible, universe-shattering secret, and, yes, all the damn omegas that keep popping up. (And, of course, omega as a reference to endings, and often cataclysmic ones.)
And I'm pretty well torn on that. On the one hand, it fits that there's some kind of big mystery and subterfuge behind the character that's been heavily implied since the late 1980's. It also adds retroactive drama to his confrontation with Rassilon in The End of Time -- or, for that matter, his confrontations with Omega in the original series.
But on the other hand, I love the idea that he's just an intergalactic vagabond who stole a ship to go see the universe, and that he only got caught up in being a heroic and, eventually, godlike figure because he kept ending up in the right place at the right time and doing the right thing.
They're not mutually exclusive, of course -- wibbly-wobbly, timey-wimey. He could have been present at the point when Rassilon and Omega perfected time travel AFTER traveling back in time himself.
Or, per the link above, some nonsense about the Other throwing himself into some damn
cloning device and reappearing as the Doctor ten million years later. But that's lame.