When I first started writing Trek books, more than twenty years ago (!), the understanding was that TAS wasn't "canon" and we should not reference it in the books. I gather things have loosened up a bit about that over the years, so that authors can sneak in references to the cartoons if they feel like it, but I still don't think it's the case where we authors have to consider TAS canon.
Some of us have done a lot more than sneak in references. Dayton and Kevin did a direct sequel to "The Time Trap" in
SCE (
Where Time Stands Still). I included a huge amount of TOS references and characters in
Forgotten History, and Devna from "The Time Trap" is a major character in my
Rise of the Federation books. Peter David, of course, has used Arex and M'Ress as regular characters in
New Frontier for quite a few years.
Excelsior: Forged in Fire did Koloth flashback chapters that were a direct followup to "More Tribbles, More Troubles."
in other words, nobody has ever told me I had change something in one of my books because it contradicted a TAS episode, as they might with a live-action episode.
True, some books do occasionally contradict TAS -- for instance, the Harry Mudd material in
TNG: The Light Fantastic seems to ignore "Mudd's Passion."
And, to be honest, I suspect some episodes are "unofficially" considered more canon than others. Most everybody accepts "Yesteryear" as part of Spock's backstory, more or less, but I'm sure there are some others that have been swept under the rug, again more or less.
One interesting case is Captain Robert April, who was first mentioned onscreen in TAS, but has been accepted as part of Trek lore for decades now, appearing in several novels and short stories. But that does not necessarily mean that the events of that particular TAS episode are "canon," if that makes any sense.
Sure, but as I said, that's true of some live-action episodes as well. "The Alternative Factor" is irreconcilable with how antimatter and dilithium are treated in the rest of the franchise, and it's the one TOS episode that virtually nobody has ever attempted to do a sequel to or reference in any way (aside from one or two recent works referencing Lt. Charlene Masters, the only worthwhile thing about the episode).
The Final Frontier's legitimacy is often called into question. "Threshold" was disowned by its own writer. And then there are details like "James R. Kirk" and "Your world of starship captains doesn't admit women" and all the times that Data used contractions in the first season, things that were unambiguously part of canonical episodes but that are still ignored as unreal because later canon overwrote them.
This is why it's a mistake to equate "canon" with "real" or "fixed" or "immutable." That's not what it means. It just means the fiction that comes from the series's own creators as distinct from other people borrowing their concepts. And those creators are free to change their minds and retcon their universes and ignore their own past works. So being part of a canon is not an absolute guarantee of permanence. Something can be part of a canon and still be apocryphal.
And yes, maybe that's a bit more often the case with TAS episodes than with the live-action series on the whole, but that doesn't mean the whole series should be disregarded. Again, canon is not permission to enjoy something. TAS is significant as the most direct continuation of TOS that exists. TOS itself is a hugely imperfect and inconsistent series with a lot of aspects of its concepts and production values and piecemeal continuity that we choose to gloss over in favor of focusing more on the whole. So why should we treat TAS any differently? Is a giant Spock clone any worse than a giant Greek god? Is the planet of accelerated cataclysms in "The Jihad" more unbelievable than the duplicate Earth of "Miri"? Are the shrunken characters in "The Terratin Incident" that much more physically implausible than the sped-up characters in "Wink of an Eye"?
I used to exclude a lot of TAS episodes from my personal continuity, considering them too fanciful, but then I realized I was applying a double standard, given how many TOS episodes have huge logic problems. So I loosened my standards and came up with rationalizations for certain things, and now there are only four TAS episodes I still find irreconcilable. "The Magicks of Megas-Tu" doesn't work because of its dependence on the discredited steady-state theory of cosmology as well as its center-of-the-galaxy setting. (The references to the center of the galaxy in ST V are sparse enough that I just ignore them and accept the rest of the movie, but it's too, well, central to "Megas-Tu.") "The Slaver Weapon" is really a Known Space story rather than a Trek story, and its version of history is irreconcilable with
Enterprise. "How Sharper Than a Serpent's Tooth" grossly misrepresents the Earth history and mythology it's based on and the chronology of ancient civilizations. And "The Counter-Clock Incident" is so damned nonsensical that even Alan Dean Foster's novelization retcons it into an illusion.
I'm wondering does it fit into the universe the crossover movie Generations or JJ movies or is it canon like the tv series? 
