Rose says that there's something a bit off about Donna - she's got a weird time signature. The Doctor says something similar, that she's prone to create new timelines. Her life is also surrounded by weird coincidences that tended to keep her out of danger; on holiday during various alien invasions etc.. There were scenes in Saturday's episode where people kept looking at Donna and half-seeing something about her - it was the time parasite, but maybe that gave them a glimpse of something else.
I can think of one other character in another show whose oddity is signalled this way - Dawn Summers in the Buffyverse. I think that like Dawn she has been inserted into the timeline with memories etc. retconned to give her a back story.
What if her name is a clue - Donna Noble = Donna Lord = Lady Lord? What if she's a Time Lord?
She's a Time Lord, hidden by the same sort of trick used by the Doctor and the Master. She was exiled to Earth to wait out the Time War, then she's going to be used to create a new timeline in which the Time Lords can exist again. Maybe there's another clue in her name - Donna = Madonna - and she is to be the mother of the new reality. Everything in seasons 1-4 has been building up to the final consolidation of apparently random factors that will allow it to happen.
I have no idea how they will resolve it, but I think the clues may be pointing this way. Could she be Romana? The Rani? Some other Time Lord we haven't previously met?
As I said, I doubt that this is right, but it's sure as hell going to be interesting finding out.