Warning Spoiler: There have been several good guesses. Many have proposed the answer to be himself, afraid of what he might do or not do, this is a popular guess since he says "Of course, who else". Another proposed answer was a young Amelia, waiting for the Doctor to come, but never arriving, this would show the similar fears between the Doctor and Amy, since that was what Amy saw in her room, they both fear that eventually, the Doctor will not return. Despite the good guesses, in Smith's final episode ("Time of the Doctor") it is revealed that he saw the crack in time. This let down many fans, as they felt that the mystery, and the hint that it was himself, was better. Other fans have said that it's a mixture of the first guess and the truth, afraid that the crack would do something more to Amy, take her away, make it so she had never even existed. Despite letting down a lot of fans, the real answer remains, he saw the crack.