* [[spoiler:AlasPoorScrappy: Mooky is very obnoxious, but he didn't deserve to die like that...]]
* AwesomeMusic: It's from the guy who did the soundtracks of Anime/GhostInTheShell, Film/DarkWater, and Manga/MaisonIkkoku, among other things.
** "Escape", the music played during the "RaceAgainstTheClock" moments.
* ItsEasySoItSucks: The game's main gameplay flaw, being that ludicrous amounts of health and ammo pickups are thrown at the player, combined with the fact that the monsters are generally very slow, also combined with the fact that the weapons available are very powerful means that the game generally has very little challenge to it.
* MemeticMutation: It's been shilled by Advertising/SegataSanshiro!
* {{Narm}}: The voice acting. All of it.
** John's particular goofy way of catching a key card in one cutscene.
** [[spoiler:There's also the matter of the mutated cow near the end of the game.]]
* NeverLiveItDown: How Commander Clansy sees his demotion from a submarine commander to leader of an underwater base. The trouble is that his "one mistake" was [[spoiler:torpedoing a passenger ship full of civilians in contested waters before a war]]. In context, his "punishment" was incredibly light. Worse, judging by the way he took it, he views ''himself'' as the bigger victim than [[spoiler:the people he killed]].
* SoBadItsGood: The voice acting. Dubois gets a shout out in-particular with his shrill falsetto fusion between Dame Edna and a South African!
* ShippingGoggles: If ''Deep Fear'' was bigger than ''Franchise/FinalFantasy'', than perhaps John and Gena would qualify. [[spoiler:If she didn't transform into an atomic beauty to defend a monkey that is!]]
* TearJerker:
** [[spoiler:Mooky's death.]]
** [[https://www.youtube.com/watch?v=4DtlMhG-toU "Old Friend"]], which plays during [[spoiler:Colonel [=McCoy=]'s HeroicSacrifice.]]
* TheScrappy: Mooky.
* TheyJustDidntCare: The translators didn't even bother to check how to spell certain names (such as "Clancy", which is spelled as "Cransy", or "STORAGE" as "STRAGE"), as it's apparent in the credits.
* UncannyValley: The FMV cutscenes, full stop. The characters' facial features just look...off. This is compounded by their unnatural, jerky movements and gestures.