In the two parter in the 5th season of Doctor Who (the new series), made up of The Pandorica Opens and The Big Bang, the Universe is "rebooted" and Amy seems to be significant in this process. When she wakes up, it's the morning after she originally left with the Doctor and it's her wedding morning. She has parents now, when they weren't present before the Universe was rebooted. Also, at this point, until she remembers him, the Doctor doesn't exist.
Are there other differences between the rebooted Universe and the original one?