I know it hasn't been long since The Power of Three aired, but I'm still surprised fandom hasn't jumped all over this, yet...
In A Town Called Mercy, the Doctor berates Rory for leaving his cell phone charger in Henry VIII's suite. We assume that this is in reference to an off-screen adventure, particularly since Rory doesn't seem particularly confused. In tonight's episode, though, we clearly see Team TARDIS hanging out in the aforementioned suite. To me, this implies that the Doctor is operating out of order-- which gives a whole new meaning to his line to Amy: "One day soon, maybe, you'll stop. I've known for awhile." It could also explain the Doctor's sudden desire to spend as much time with Amy and Rory as possible, even if it means sitting still.
I suppose it's possible that A Town Called Mercy takes place after The Power of Three for Amy and Rory as well, but I'm not sure what the point of that would be. (EDIT: I suppose A Town Called Mercy could also take place during TPoT, although, again...why?)
Anyway, it's pretty heartbreaking, when you think about it.