* CutSong:
** "[[https://www.youtube.com/watch?v=P-RdTjI5bmg Wind Fortress]]"[[note]]Later readded to the game as the song to a bonus level within the UpdatedRerelease[[/note]], "[[https://www.youtube.com/watch?v=KO9pcsRzMxE People of the Root]]", "[[https://www.youtube.com/watch?v=L77txcf-M4Y Plant (B)]]", and "[[https://www.youtube.com/watch?v=RpVcM4peIkM Pier Walk]]". There are also beta versions of at least ten songs.
** There's also the [[http://www.mediafire.com/?dnfgttxqqzm midi versions]] of all the songs in the Wii version. YMMV on whether they sound better than the final instrumented versions, but according to the composer for the remixes, the final versions sound little like he intended. Also includes some tracks that didn't make it to the final version, such as a version of "Plantation" that uses the main theme in a style more similar to "Plant."
** To a lesser extent, the expanded portion of the song "Zombie" as heard within ''Guxt'' and ''Kero Blaster'' as evidenced in the way the song's stored within the song file[[note]]Two of the assigned instruments within the song go unused. They sound identical to the instruments exclusively used within the aforementioned expanded version of the song[[/note]].
* DevelopmentGag: In [[https://www.cavestory.org/game-info/beta.php an early version of the game]], all enemies are shaped like bars of soap. Balrog is likely a remnant of this idea, as is Puu Black, the ghost in the clinic in the Labyrinth. Furthermore, "Puu" was Balrog's early name.
* DuelingDubs: [[invoked]] There are ''two'' major English translations of Cave Story. The original translation by [[https://agtp.romhack.net/ Aeon Genesis]],[[note]]notably with assistance from [[ApprovalOfGod Pixel himself]][[/note]] and the translation by [[Creator/{{Nicalis}} NICALiS]], which distributes the commercial versions of the game. The [=NICALiS=] translation is known to be more accurate overall, at least naming-wise, but the script occasionally feels [[BlindIdiotTranslation overly literal]], while the Aeon Genesis translation does a better job conveying emotion.
* DummiedOut:
** The character portraits displayed during dialogue include one for [[spoiler:Sue as a human. Since Sue doesn't turn back into a human]] until the end credits, the sprite goes unused.
** There's unused sprite sheets for a Mimiga soldier, a Mimiga watching a TV or computer, a Mimiga with a yellow shirt, and a guy smoking a cigarette.
** There is one dummied out area in the game listed as Cook.pxm in the game's files. It is an empty room similar to many of the Mimiga houses. What makes this more interesting was that it was last modified August 7, 2002, two months before Pixel restarted development.
** You can find an unused weapon by modifying any of the game's scripts to give you said weapon at some point.
** One can also find the Beast Fang hidden under the HeartContainer in the plantation area of Mimiga Village. It's still in the remakes, [[DevelopersForesight and its description has been changed to say that you shouldn't have it]].
** There are instruments assigned to melodic channels "0" and "5" within the song "Zombie" that correspond to the instruments exclusively used within the expanded portion of the song from both ''Guxt'' and ''VideoGame/KeroBlaster''. Said channels are unused within the ''Cave Story'' version of the song due to it lacking the aforementioned expanded portion.
** The Nintendo Switch port has [[https://tcrf.net/File:Cave_Story_US_Switch_Buttons.png unused button mapping icons]] for the Platform/PlayStation4, Platform/XboxOne, Platform/PlayStationVita, and Platform/WiiU, none of which got a port of ''Cave Story'', but they may have originally been planned to.
* FanWorkBan: Late November 2020, [=NICALiS=] issued a [[https://github.com/github/dmca/blob/master/2020/11/2020-11-19-nicalis.md DMCA takedown]] of fan-made reverse-engineered ports of the freeware version, [=CSE2=] and Cave Story Tweaked, removing downloads of their binaries, source code, and forks thereof.
* KeepCirculatingTheTapes: The game itself doesn't qualify for the most part, but two specific versions, the Platform/WiiWare and the Platform/Nintendo3DS versions, became this due to both services not allowing any new owners to purchase any games as of March of 2018 and March of 2023 for both services respectively. The only way to play these versions without having purchased it back then is piracy at this point.
* NoExportForYou: The Platform/WiiWare version of the game has never seen a release in Japan, and, due to the shutdown of the Wii Shop Channel, never will, which is ironic since that's where the game was made. However, it has seen a European release.
* ShrugOfGod: ''Cave Story'' ends rather neatly, but it's never fully explained just what the island is, or why the surface tried to attack it (according to Curly, the surface was trying to [[spoiler:get a hold of the Demon Crown]], but for what purpose isn't clear). Additionally, according to Jenka [[spoiler:there is a rumor that the Mimiga who retaliated by ingesting red flowers were unleashed onto the surface]]. In the latest remake, [[spoiler:it's revealed in a possibly canon sequence that someone or something was making Curly clones in the Wind Fortress]]. Who and why has not been explained. Pixel was asked about these things in an interview, and this was the reply:
--> "The story of Doukutsu only hints at the world in which the game takes place. How much of this world have you created that we don't see in the game? Will we get to see more of it later on?" - [=TIGSource=]
--> [[https://web.archive.org/web/20050806080152/http://www.tigsource.com/features/interview_pixel.html "Nothing of that world exists beyond what you see in the game, as I don't have the skills to construct anything further. I leave the details of Cave Story's world to the player's imagination."]] - Pixel
* WhatCouldHaveBeen: [[spoiler:Quote]]'s original name was going to be "Curly Brace". Then someone mentioned to the developer that it sounded feminine to Anglophones, so he changed it.
* WordOfGod: According to [[https://www.youtube.com/watch?v=w8XINfralSE this video,]] Balrog is [[spoiler:a bar of soap twisted beyond recognition.]] [[https://web.archive.org/web/20121127114746/http://hpcgi2.nifty.com/rochet/bbs/bbs0003.cgi He also said]] that King has red eyes "by red flower" which he ate "for the power" and didn't go rabid because "he may have cooked it."
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