* AwardSnub: It received three UsefulNotes/AcademyAward nominations and won none. It wasn't nominated for Best Picture, Actor, Actress or Supporting Actor.
* SugarWiki/AwesomeMusic: Music/CarterBurwell's haunting, minimalist score, which manages to get incredible mileage out of a six-chord {{Leitmotif}}.
* CrossesTheLineTwice: One actor playing a fan was told to work in the word "retard" as much as possible in his brief scene with Malkovich. Which he did.
* {{Fanon}}: It is widely agreed that Dr. Lester's name (never given) is "Moe."
* HilariousInHindsight:
** Throughout the film, lots of characters praise John for being in a "jewel thief movie", which he flatly denies, and this was true at the time. Later, he was in ''Film/JohnnyEnglish'', where he played the BigBad who has the British Crown Jewels stolen as part of his plot to take over the UK.
** Creator/CharlieSheen is the friend Malkovich talks to when he feels like he's going crazy, and needs a sane man to bounce ideas off of. Yup. (This was long before his 2011 breakdown.)
* MemeticMutation: "Malkovich Malkovich Malkovich."
* NightmareFuel[=/=]ParanoiaFuel: Anyone could be watching what you're doing now, and you wouldn't even know it. Might want to check what tabs you have open...
* QuirkyWork: The plot involves people entering a portal into Creator/JohnMalkovich's brain and temporarily taking over his body. Creator/JohnMalkovich reacted to receiving the script with IsThisAJoke and didn't dial down anywhere down the line.
* SignatureScene: The Malkovich Restaurant scene quickly became the most well remembered moment from the film thanks to it exemplifying its distinctive blend of SurrealHumor and SurrealHorror by featuring an entire crowd of Malkovich lookalikes who can only say his last name.
* TearJerker: All of it.
** Malkovich's joy at [[spoiler: being freed from Craig's control]]... only moments before he's [[spoiler: permanently taken over by Lester and his gang.]]
* TooBleakStoppedCaring: ''Every single character'' is a self-centered jerk -- save the eponymous Creator/JohnMalkovich himself, who just wants this madness to end and for everyone to get out of his head [[spoiler:which never happens, as the movie ends with his body being permanently occupied by all but three of those self-centered jerks ''simultaneously''. And even ''he'' gets painted as a little bit of a pervert. At least Craig, who ''started'' the whole mess, gets left in the lurch while both the women who he pursued live HappilyEverAfter... though they're both self-centered jerks too]].
* UnintentionalPeriodPiece: Not as bad as most instances, but nonetheless fairly noticeable. Going past the elephant in the room of the 1973 World Trade Center being visible in one shot, almost every TV in the film is an analog 4:3 CRT, with the only widescreen LCD being seen in Malkovich's apartment; LCD televisions had been out for roughly a year by the time the film released, but were a considerable luxury if only due to how nascent the technology was. Just ten years later, LCD monitors would become a mainstream commodity, with CRT televisions fading away outside of particularly niche or ''very'' low-income markets. Additionally, characters communicate on the phone exclusively via corded landline phones rather than cell phones, which were also still something of a luxury at the time, and Craig seeking out job offers through the newspaper readily dates the film to an era before the internet became a mainstream utility; it already existed for years by 1999, but was still fairly niche in terms of usage. By the film's 20th anniversary, job listing sites would become a much more common means of seeking out work.
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