Yes Thanos does reference it in his solo series which is why I tend to think of it as canon, but the editors at Marvel have come up with some horribly convoluted way to explain it and still make The End not canon, something like it all happened in another universe (not 616). I think its just easier to accept it.
Yes its Cannon, Thanos mentions it in his solo series to Adam Warlock, and thanos solo series has to be cannon because at the end of his series he has meet up with fallen one, and Starlord has left the super prison thing where oblivion was being held.
They might be able to say that, the End wasnt cannon, but then that would mean that thanos solo series wasnt cannon and neither is all of Annihilation...which im pretty sure is...
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<<This is what Andy Schmidt who is an editor from Marvel and currently working on Annihilation had to say about Marvel: The End.
"Someone else answered this later, but just so you get it from me as well: MARVEL UNIVERSE: THE END is an out of continuity story, however, Thanos does refer to some "event" that seemingly bore a similar resemblence to the THE END story that occured some time in between INFINITY ABYSS and THANOS #1."
Also in Akhenaten's profile in OHOTMU A-Z #1 in 2006 it says that he is from the Earth-4321 reality. And it also states "At least some of Earth-4321's events may have occurred in the Earth-616 reality, but the extent of this duplication remains unrevealed." http://img189.imageshack.us/my.php?...khenatenxl9.jpg
All the other "The End" books were not canon and more of a what if. But the event that happened in Marvel: The End were hinted to in Thanos solo comic and also in the profile for Thanos in Annihilation.>>