Warning: Spoiler alert! This whole thread is spoilers until it's derailed.
Okay, so at first I've thought the hidden things throughout the season were the cracks. It made sense, they were in every episode (except in ones after they're fed it seems). Now yes, this seems like season 9's bad wolf, leading to the main villain of the story arc, but I think there's something else there. There seem to be quite a lot of specific references to older doctors, mostly pictures.
1 - "The Eleventh Hour" - All the doctors' pictures shown by the Atraxi
2 - "The Beast Below" -
3 - "Victory of the Daleks" -
4 - "The Time of Angels" -
5 - "Flesh and Stone" -
6 - "The Vampires of Venice" - William Hartnell in the psychic paper
7 - "Amy's Choice" -
8 - "The Hungry Earth" -
9 - "Cold Blood" -
10 - "Vincent and the Doctor" - The first and second doctor are printer by the doctor's mirror analyzer thing.
Yeah, it's sparce, but maybe there's more? In "Cold Blood" the doctor references the fifth's celery stick. I didn't add it because I think that the theme is pictures. Maybe I'm looking too much into random homages :\ But there's a chance this is leading to some sort of pan-doctor encounter at the end of the season, which wouldn't be too out there if you think about what the doctor pulled out of the crack.
Did you guys find any more pictures? I'm not very good at the spotting game :3