As promised by Steven Moffat and Matt Smith, in the first episode there were a few clues at to the arc of series and the final two episodes of this series.
The first and most obvious, is the statement made by Prisoner Zero:
"The cracks in the skin of the universe – don’t you know where they came from? You don’t, do you? The Doctor and the TARDIS doesn’t know. The universe is cracked. The Pandorica will open. Silence will fall."
As Prisoner Zero is taken away by the Atraxi it tells The Doctor:
"Silence Doctor. Silence will fall!"
The crack in Amy's bedroom wall may have more meaning then was first thought:
Just a crack, well we all thought so, until Prisoner Zero told us the universe is cracked.
And did anyone notice the shot of the console screen? A shot which was focused on for a little longer then it should have been. Well if you look at the image of the crack on the wall and the image of the console screen, you can see that the lines are very, very similar. They aren't an exact match, but they are pretty close.
Jeff's laptop might be a clue to the arc and the series final:
The word myth was clearly displayed on the bottom of the laptop screen. But the Y was a little different, it was the Greek symbol for PSI (Ψ). This could feed into a greek mythology theme and Pandorica – Pandora’s box. And what happens if you open Pandora’s box…