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So far as I can tell, some did, some didn't, and which did depended on Amy's memory. Others may be able to give more detail.

Obviously there wasn't a huge amount of detail given on-screen. We haven't seen any 21st century humans confronted with aliens (other than Amy and Rory) since "The Big Bang".

However, behind the scenes, Steven Moffat has confirmed that his intention is that the events that were erased by the cracks are gone for good after the reboot, and that includes all of the publicly-known invasions of 21st century Earth, so humans in the 2011 Whoniverse will be as surprised by aliens as humans in the 2011 real world would be. Elsewhere, he's said that he wasn't erasing the entire last 5 years of the show. That's about all he's said.

So, fans can only guess exactly what was changed. If you take Moffat at face value, I'd say that "Aliens of London" / World War III, "The Christmas Invasion", "The Stolen Earth" / "Journey's End", "The Next Doctor", and "The End of Time" from the RTD era are probably on the list, and maybe Age of Steel / "Doomsday", the Torchwood story Children of Earth, and the classic-series story "Terror of the Zygons"*. (And some of the New Series Adventures novels, if you believe they count in the first place.)

If you want to know why the cracks ate the 2009 Dalek invasion but not the 2010 lone Dalek running around a secret compound, that's a good question that Moffat hasn't answered (and probably won't). I can come up with half a dozen good theories, but my current favorite one is this: We know that some major pieces of Earth history are a "fixed points in time". Changing these takes a lot of energy, and causes a lot of damage to the "web of time". So, assuming Earth wasn't "supposed" to be invaded by aliens ever Christmas for 5 years, each time that happened, it was a "complicated space-time event". And we know that's exactly what the cracks were attracted to. So, the very things that made the Whoniverse most unlike our universe (or most unlike the Whoniverse of the classic series) were the ones most likely to be erased.

  • The reason I include Terror is that in an earlier comment by Moffat that "Nessie in the Thames" was the only classic story that couldn't be explained away or covered up. Many fans have pointed out that "Revelation of the Daleks" implied that it had been explained away, but clearly Moffat didn't remember that, so he wouldn't have taken it into account.