I'd assume they'd be a big part of the 'Fall of the Eleventh'. Madame Kovarian's still about somewhere/sometime, and unless the TARDIS exploding was 'Silence falling', we still have that to come as well. I expect them to play a big part in Eleven's future (Or lack ofWatched a bunch of series 1-3 stuff with roommates last night, including The Empty Child/The Doctor Dances, The Girl in the Fireplace, and Blink. I miss creepy Moffat. I really hope we see the Silence again and not just as window dressing in an everything-but-the-kitchen-sink finale.
Speaking of 'Silence will fall', does anyone think that might have to do with the Doctor being wiped from history/records rather than the Silence themselves? It makes sense IMO, and it seems like something Moffat could do (Assuming he hasn't forgotten about it). Of course it could have just been about the events of Day of the Moon/The Impossible Astronaut, considering the Doctor remembered that comment when he first made contact with the Silent's.
Gah, it's been too long since the Christamas special, I need more Who! It's coming back this month, right?