* ContinuityLockOut: Several episodes of the animated series call back to or serve as continuations of episodes from the original [[Series/StarTrekTheOriginalSeries 1966 live-action series]], so it would be wise to watch at least the majority of ''The Original Series'' before viewing this series.
* DracoInLeatherPants: "The Magicks of Megas-Tu" -- to clarify, the episode provides an AlternativeCharacterInterpretation of a being who claims to have inspired the Biblical figure of {{Satan}}.
* EnsembleDarkhorse: Lt. M'Ress, for [[CatGirl fairly]] [[UsefulNotes/FurryFandom obvious reasons]].
* HilariousInHindsight: Reruns of the show aired on the fledgling Creator/{{Nickelodeon}} in the late 80s and early 90s. Come 1994, and [[Creator/ViacomCBS Viacom]], owners of Nick, bought Paramount (however, it would take until 2021, after a de-merger and re-merger separated Nick and most of the franchise, for an original ''Trek'' show to be produced for the channel -- ''WesternAnimation/StarTrekProdigy'').
* MagnificentBastard: "[[Recap/StarTrekTheAnimatedSeriesS1E8TheMagicksOfMegasTu The Magicks Of Megas Tu]]": Asmodeus is a leader on the planet Megas Tu. The Megans came to Earth hundreds of years ago to use their magic to help humanity but were [[WitchHunt persecuted]], leading to the [[SalemIsWitchCountry Salem witch trials]] and causing the Megans to flee Earth and became distrustful of humanity. When the ''Enterprise'' accidentally discovers Megas Tu, one of the Megans, Lucien, helps the ''Enterprise'' crew. Asmodeus puts the ''Enterprise'' crew on trial for the crimes of humanity, in a setting similar to the Salem witch trials. Asmodeus allows Spock to defend humanity and Asmodeus studies the ''Enterprise'''s records and concludes humanity has changed, but declares Lucien a traitor for helping them and intends to send him to Limbo forever. Kirk defends Lucien and Asmodeus reveals that Lucien is really [[{{Satan}} Lucifer]] and asks if he still will defend him and Kirk says yes, causing Asmodeus to battle Kirk for the fate of Lucien, though ultimately [[SecretTestOfCharacter this was all a test]] to see if humanity had truly changed.
* MemeticMutation: Kirk's DullSurprise reaction in one episode is a fairly common meme for when one is feigning surprise.
* {{Narm}}:
** Sometimes the limited number of voice actors could make things a little silly, as in "The Lorelei Signal," when Creator/NichelleNichols and Creator/MajelBarrett have to voice, like, seven different people.
** For some reason, there's a shot of Kirk's face being '''too close to the screen''' several times an episode. (Was this Creator/WilliamShatner's idea?) Other characters get awkward closeups too, so it's more likely Filmation realized that filling the screen with someone's face needs less animating than the Enterprise's machinery.
** "Mudd's Passion" strains so hard to not play into the already legendary HoYay between Kirk and Spock when they're both hit with a love potion, which backfires spectacularly as they proceed to act very physically affectionate while also insisting they're "best friends," distinctly coming off as a SuspiciouslySpecificDenial.
* OutOfTheGhetto: It was a continuation of the live-action ''Series/StarTrekTheOriginalSeries'', with Creator/GeneRoddenberry at the helm, scripts by many of the same writers, and the original cast (except Creator/WalterKoenig) providing voicework. The show takes itself just as seriously as the original, with no concessions to its possibly younger audience. Stories included an episode about religious intolerance titled "Jihad", and another in which Nurse Chapel gets a whiff of Harry Mudd's love drug and tries to jump Spock's bones (or at least as close to it as TV would allow back then). It was well received enough to earn the franchise's first UsefulNotes/EmmyAward. This is remarkable when one considers that the company that made it, Creator/{{Filmation}}, to at least some extent actively encouraged the AnimationAgeGhetto, as they felt it their civic duty to act as agents of social uplift for the kids, and not to scare or puzzle them too much. And yet, it aired in the 1970s on Saturday morning -- anything not kid-friendly in those slots was literally forbidden back then. Perhaps Roddenberry's influence was enough to overrule Filmation head Lou Scheimer -- and considering the franchise's social bent to start with, it's possible that may have swayed him.
* PopularWithFurries: M'Ress was one of the first, if not ''the'' first recognisably anthropomorphic "furry" character (neither [[LittleBitBeastly a human with cat ears]] nor [[FunnyAnimal a bipedal, talking animal]]) to appear on TV.
* ReplacementScrappy: A mild case with Arex who, while nowhere near as actively disliked as several other characters from the franchise, is seen by many as a bland, uninteresting character, who is only noteworthy for a mildly BizarreAlienBiology and doesn't do a particularly good job of filling the shoes left vacant by Chekov.
* SuspiciouslySimilarSong: Filmation was unable to use the original theme song, so the opening theme for the animated series was a new song that almost sounded like, as Website/TheAgonyBooth put it, "the TOS theme played sideways".
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