6. Eggs/Christmas/Lights
It was one "arc" that drove Who fans crazy last year - well, apart from guessing which order the episodes were in - but it was never properly resolved or mentioned in-universe. Why were there so many references to eggs, Christmas and flickering lights? There was the question of where Oswin got her eggs for the soufflés, dinosaur eggs and Jex's egg-looking spaceshift, as well as the Doctor mentioning Christmas at least twice, and scenes of Amy and Rory at Christmas. And then there was the surely-not-coincidental simultaneous quivering of any electric light in most episodes. Most fans gave up trying to decipher the meanings of the "clues", but really, it's quite simple. It was just foreshadowing. The next few big events in Who were to be the Pond's departure, the Christmas episode, and the introduction of a new companion at Easter. If you've been noticing one too many Rose references - 'Hungry Like the Wolf' was somewhat of a giveaway - then just look at who's returning for the 50th.