I think we're meant to assume it was one of the Silence (they seemed to change the voice between episodes). The Silence trying to kill the Doctor by blowing up the TARDIS (to prevent The Question from being asked at Trenzalore) inadvertently caused the cracks in time. Their other attempts to kill the Doctor were of course Lake Silencio and the Judas Tree poison. As time isn't linear, particularly in Moffat's Who, it may be that these attempts, from the Silence's perspective, didn't happen in the same order that we saw.
I think that is very likely what happened, and now that it's several years later, I'm pretty much over it, and I doubt it will ever be truly explained. At the time, though, I really wanted it to be a specific person. Part of me hoped that it was River that caused the explosion, perhaps unaware she was doing it as part of her evil programming. She was the only one onboard, afterall.
That's what I like to think. Whether or not that was in Moffat's head at the time, it ties up very nicely. There's certainly nothing to disprove it. What I'd have liked to see explained was the eerie silence falling over the Venetian market, with the populace disappearing suddenly...
It's one of my pet peeves of Moff's tenure, way too many unanswered questions, eg, we see Amy's parents... and then they promptly vanish again. Or "Silence will fall" Or the TARDIS exploding. He's too distracted by the next shiny thing.
I agree with the point, if not the first example. Amy's parents vanish because they're not important again.
What point was there in showing her parents? We saw they returned to the void, and her childhood with them had been restored, why would we need to see them when Amy was an adult after that? This is no different, IMHO, then a Companion leaving, and seeing them again. Now, about the TARDIS explosion, yea, if he's done with that, and not planning on revisiting it as an open mystery, then, that's certainly a legitimate gripe. Though, he may yet revisit it. We were just introduced to The Great intelligence, an enemy that hasn't been seen since Troughton's era, there could be a great big arc tied to the Great Intelligence (It could be behind the Silence, The exploding TARDIS, The Mystery of Claras, The Fall of the 11th....) I'm not saying The Great Intellignce is behind everything, but, it's not out of the question.
This is one of the reasons I was glad they didn't film the Brian Coda, because it's great that he gets to find out about them, but what about Amy's parents and Rory's mum? At least Brian would have some idea what's likely happened to them which gives him more closure than they got. For them presumably Amy and Rory just vanished! I like to hope that Moffat hasn't fogotten about the voice...