For pretty much the entire history of the franchise there have been stories that have come out only to be contradicted later on. I was just curious to see which versions of these stories people liked better. Some of the best and most popular examples I know of would be all of the different versions of the Mirror Universe, the three (or is it more) versions of the TOS Enterprise crew's first mission, the Klingons or Romulans. The only ones I really have experience with are the different versions of the Mirror Universe, and of five I have only read the TOS Mirror Universe Saga comics and the MU series. My favorite of those was TSoE, although I did really enjoy the comics too. I've also seen/ read two versions of the first TOS Enterprise mission, ST09 and All Those Years Ago. I think these two were pretty close, but since I don't remember ATYA very well at all I have to go with ST09.
Oh, and feel free to include stories that are purposefully marked as alternate universe stories like the MyrU stories, or even Mirror versions of Prime universe events.
Oh, and feel free to include stories that are purposefully marked as alternate universe stories like the MyrU stories, or even Mirror versions of Prime universe events.