nobody's ever told me there was a problem with doing so. I can't believe there are any trademark/copyright issues when TAS is available on home video and Netflix right alongside all the live-action series; as far as I know, it's now fully owned by CBS (formerly Paramount). And I believe Roddenberry's Norway Corporation (Lincoln Enterprises was his mail-order memorabilia company, not his production company) sold all the rights to ST to Paramount a long time ago.
Exactly. When he was vetting tie-in manuscripts for Roddenberry (i.e. 1986-1991), Richard Arnold would enforce the comment by the Okudas (in the Encyclopedia and Chronology) that Roddenberry had asked that Filmation's TAS no longer be referenced, although they got permission to add Robert April, from the first TV series proposal (and with Roddenberry's head Photoshopped onto Pike's torso), and info about ShiKahr and Spock's childhood from "Yesteryear". Similarly, Robert Greenberger's editorial in DC Comics' post-TOS Series 2 adventures (issue #1) explains how the 1989 memo had requested that Arex, Mress and TAS no longer be referenced.
The first new reference to TAS came just after Roddenberry's passing. Jeri Taylor briefly mentioned the Phylosians (from "The Infinite Vulcan") in her novelization of TNG's "Unification".
My annotated list of TAS references desperately needs updating but is at:
http://andorfiles.blogspot.com.au/2009/10/toon-trek.html
TAS has never been considered canon because it was not filmed, but rather animated. Who decided that? I dunno. But if you talk to most fans they will say that it's not.
Not quite. Bjo Trimble's first commercially published "Star Trek Concordance" (Ballantine Books) embraced TAS with complete approval of Gene Roddenberry and DC Fontana, and included official b/w Filmation artwork. It was definitely canon during the 70s and early 80s.
But, by 1989, several things had changed. Fontana and David Gerrold had fallen out with Roddenberry over co-creatorship of TNG and there was a court case (settled out of court for undisclosed sums), Filmation was selling off its assets, all of Filmation's productions were in ownership flux, and Larry Niven was trying to sell the kzinti and "Known Space" as a roleplaying game, and a book series, "Man-Kzin Wars".
Richard Arnold's argument in 1989 - that TAS was merely licensed out from Paramount (to Filmation, Norway Corp
and NBC's Children's Programming) - meant, in the then-opinion of the Star Trek Office, it was actually no different to the various licensed comics, novels and RPGs. It was a handy way of resolving the fact that leaving it as canon would be an annoyance for scriptwriters of TNG, since most of those writers had no knowledge of those 22 stories that hadn't been widely aired on TV for many years. But it meant DC Comics had to shed Arex and M'Ress as regular characters, and cameos of TAS elements were frowned upon in the books.
It became very easy to say "Canon = Live action", and he tried to do that often at conventions in the 90s and his columns in "The Communicator".