* AntiClimaxBoss: Prince Thrakhath in the final stretch of ''Wing Commander III''; even though he is flying the Bloodfang, renowned for its unmatched lethality among the Kilrathi, he flies little faster than a Vaktoth and you likely won't need much time taking him out in your Excalibur.
* FandomRivalry: The fandoms of ''Wing Commander'' and ''VideoGame/{{Freespace}}'' have at times butted heads, influenced in part by personal dislikes.
* FanonDiscontinuity: Depending on who you ask, one or a combination of the following: ''Prophecy'' and later games, the novels, the movie, the cartoon, and in rare cases, ''Wing Commander'' III and IV.
* GrowingTheBeard: While the main campaign of the first ''Wing Commander'' and the first ''Secret Missions'' expansion pack were miles ahead of anything else available in the early 90s in terms of graphics and game play, the storyline is little more than an ExcusePlot. In ''Secret Missions 2'' the characterization and plot both become much more engrossing. We first meet several recurring characters in [=SM2=], both heroes and villains.
* HarsherInHindsight: ''Wing Commander III'' opens on the burning, half-sunken wreck of the ''Concordia'', your flagship from the previous game which is then deemed a "total loss". Come 2012 the ''Costa Concordia'' disaster took place, with the ship similarly marooned and damaged beyond repair off the coast of Tuscany.
* RetroactiveRecognition:
** Josh Lucas and [[Creator/FrancoisChau François Chau]] in ''Wing Commander III'' (and ''IV'' in Chau's case)
** [[Series/IronChefAmerica Mark Dacascos]] in ''Wing Commander IV''.
** In a blink-and-you'll-miss-it minor scene, you can see that the pilot who offers to carry Blair's bag when he first arrives aboard the ''Lexington'' is none other than [[Film/StarshipTroopers Casper Van Dien]].
* TheScrappy: Everybody seems to hate Maniac (both in real life and in-universe)... [[CreatorsPet Except for the writing staff]], since of all of the cast members who get KilledOffForReal, Maniac -- the most likely candidate given his rank, status, and [[LeeroyJenkins reckless behavior]] -- isn't one of them.
* {{Squick}}: From ''Wing Commander IV'', the sight of one of the victims of the biological attack on Telamon. Even Blair and his comrades must look away upon seeing the aftermath of it.
* StoicWoobie: Mariko "Spirit" Tanaka and Michael "Iceman" Casey both have lost loved ones to the Kilrathi (fiance and family, respectively), but don't go wallowing in self-pity over it.

* ExecutiveMeddling: Unusually, a case where some executive meddling would have made the film ''better.'' [[WordOfGod Roberts]] later said that in hindsight, he wished he'd had an executive producer who could have told him the elements of the film that were distracting from the core story and needed to be removed, especially on the tight budget ($27 million, expanded to $30 million after Roberts kicked in an additional $3 million out-of-pocket).
* HilariousInHindsight: Blair in the video games was portrayed by Creator/MarkHamill, best known for playing a [[Franchise/StarWars Jedi]]. Blair in the film is played by Freddie Prinze Jr., who would [[WesternAnimation/StarWarsRebels go on to play a Jedi]].
* TheyChangedItNowItSucks: A ''very'' common complaint, particularly the name of the carrier changing from TCS ''Tiger''''s''' Claw'' to TCS ''Tiger Claw'' due to script editing confusion between editors for the film.
* WTHCostumingDepartment: The Kilrathi look ''nothing'' like their video game counterparts and in fact are visibly ''furless''. Chris Roberts himself admits that he was satisfied with neither their look in the games or their redesigned appearance in the film.

[[AC:Wing Commander Academy]]
* FoeYay: An occasional element of Maniac and Archer's UST.
* SpiritualLicensee: To Universal's previous sci-fi cartoon, ''WesternAnimation/{{Exosquad}}''; indeed, USA Network aired reruns of that show the same time they were airing this one.