The James Bond films had the evil organisation SPECTRE, which was the SPecial Executive for Counterintelligence, Terrorism, Revenge and Extortion.
Probably subverted with the fancy-sounding but not acronymmy QUANTUM.
Memorably homaged in Carry On Spying, which featured the evil organisation STENCH (the Society for The Extinction of Non-Conforming Humans) and the more ambiguous SNOG (the Society for the Neutralising Of Germs..."I've always fancied doing a bit of SNOGging, meself!").
Kevin Smith's Jay and Silent Bob Strike Back feature the Coalition for Liberation of Itinerant Tree-dwellers, described as an offshoot of the Liberate Apes Before Imprisoning Apes movement. (Justified in-universe. The members of C.L.I.T. ask Jay to describe his cunnilingus technique on-camera, and send the video to the news media to set Jay up as the "C.L.I.T. Commander".)
Making for an...interesting...news report on their actions...double entendre, here we come...
The CLIT does not exist. By the way, in Real Life, there's Moro Islamic Liberation Front.
Intolerable Cruelty features the National Organisation for Matrimonial Attorneys Nationwide, which boils down to NOMAN, although to do so it has to repeat the part about being national. This seems kind of irrelevant until you find out the organisation's slogan: "...let NOMAN put asunder".
The Naked Gun 2˝: The Smell of Fear movie featured several organizations opposing solar power with names that result in incredibly ironic acronyms: the Society of Petroleum Industry Leaders (S.P.I.L.); the Nuclear Power industry's Key Atomic Benefits Office Of Mankind (K.A.B.O.O.M.), and the Society for MOre Coal Energy (S.M.O.C.E.; that is meant to be pronounced "smoke").
In the satirical movie Team America: World Police, it was quite simple for the filmmakers to change the name of the Screen Actors Guild — which already has a pretty unfortunate acronym — to the Film Actors Guild.
How could you forget I.N.T.E.L.L.I.G.E.N.C.E.?
When Agent Coulson of S.H.I.E.L.D. first appears in Iron Man 1, he doesn't use the acronym of his organization when talking to Pepper. The best part is, apparently they didn't notice the coincidence:
Coulson: I'm Agent Phil Coulson with the Strategic Homeland Intervention, Enforcement and Logistics Division.
Pepper: That's quite a mouthful.
Coulson: I know, we're working on it.
In ROTOR (a horrific B-Movie rip-off of Robocop), the title character stands for Robotic Officer Tactical Operation Research.
In The Blues Brothers, the brown-shirted group of Illinois Nazis led by Henry Gibson is the American Socialist White People's Party ("Asswipes"). The acronym is an Stealth Pun which doesn't appear in the film.
Deliberately averted, meanwhile, with the State County Municipal Offender Data System.
People who weren't fans of the Star Wars prequels had a ball with pointing out the acronym of episode III to be Star Wars: ROTS.
In the James Bond spoof Our Man Flint, Derek Flint is a former agent of the Zonal Organization for World Intelligence and Espionage. He battles the evil organization Galaxy, which in a relative stroke of creativity, appears not to be an acronym for anything.
The Cat also had the riding-mower-style house cleaning device, the Dynamic Industrial Renovating Tractomajiggar.
C.H.U.D. stands for Cannibalistic Humanoid Underground Dweller, and is a lot of fun to pronounce. Well, it actually stands for Contaminated Hazard Urban Disposal.
Everyone knows that HAL 9000 (Heuristic/Algorithmic), the sentient computer in the movie 2001: A Space Odyssey is named such that if you take the next letter after each letter in its name, you get IBM. Leonard Wheat, in his book Kubrick's 2001: A Triple Allegory, argues that this is not a coincidence (in spite of Arthur Clarke's insistence). Wheat plausibly explains the origin of the 9000 in the name, and also goes on to argue (convincingly!) that the moon monolith's official designation of TMA-1 should actually be spelled "TMA ONE" and is an anagram for "NO MEAT". Wheat's web page suggests that the AE in the troublesome "AE 35 unit" in the film stands for Aeolus. Big fun with acronyms.
Incidentally TMA stands for Tycho Magnetic Anomaly, since the first monolith was buried in the Tycho crater on the moon and was discovered only because it produced odd readings in the moon's magnetic field. This mentioned only in the book (kinda self-explanatory, though).
The film Godzilla vs. Space Godzilla had the giant robot named M.O.G.U.E.R.A which stands for "Mobile Operation Godzilla Universal Expert Robot Aero-Type." The full title was basically applied to the name of the Mogeras from The Mysterians, which wasn't originally an acronym.
In the comedy J-Men Forever (1979) the F.C.C. (Federal Culture Control), KRAP Radio, and M.U.S.A.C. (the Military Underground Sugared Airwaves Command) join forces to broadcast schmaltzy music to counter the rock & roll invasion of Earth. And there's Billy Batson Batchit, who becomes The Caped Madman (a re-dubbedCaptain Marvel) by uttering the magic word "SH-BOOM!", enabling Billy to "take on all the vices of a J-Man of the Secret Service: S for Sneaky, H for Hateful, B for Bigotted, O for Obnoxious, another O for Double-Obnoxious, and M for Mean!"
In the Watchmenmovie, Adrian Veidt/Ozymandias uses a device called "SQUID" to destroy New York City and several other cities. What does "SQUID" stand for? Sub-Quantum Intrinsic Device. "The squid" is the fan name for the giant tentacled alien creature that destroys NYC in the original graphic novel, and the name was inserted into the movie either as a Mythology Gag referencing the book's original ending or a salt-in-the-wound attack on an overprotective fanbase.
The G.I. Joe movie, G.I. Joe: The Rise of Cobra, has a lot of changes from the source material (much to fans' displeasure), one of them being that the "Real American Heroes" are now international. "G.I. Joe" was a reference to World War II-era General Infantry units, with "Joe" a generic moniker; with the name retained for the movie despite the "American" part going out the window, the creative minds behind the movie decided to shoehorn in an appropriately awkward acronym. Feast your eyes upon the Global Integrated Joint Operating Entity!
Actually, GI seems to have started out as an abbreviation for 'Galvanised Iron' military equipment, then for 'General Issue' equipment and adopted in that sense by the troops for themselves, not 'General Infantry.'
In The Avengers (1998), one of the Villain organizations is named the British Royal Organization for Lasting Liquid Years. "Brolly" is British slang for "umbrella", which is appropriate since the plot of the movie involves weather control.
Accepted dealt with the exploits of a group of would-be college freshmen, who after being rejected from all the colleges and universities to which they had applied, proceed to "create" their own "college": The South Harmon Institute of Technology (S.H.I.T).
Undoubtedly derived from the persistent urban legend that claims that a Texas college was nearly named the Sam Houston Institute of Technology (or Teaching).
In the 1987 film remake of Dragnet, starring Dan Aykroyd and Tom Hanks, they uncover a sinister organisation named 'P.A.G.A.N.' - People Against Goodness And Normalcy.
Parodied in Cloudy with a Chance of Meatballs with the Flint Lockwood Diatonic Super Mutating Dynamic Food Replicator, or FLDSMDFR. Flint insists on pronouncing the acronym despite how confusing it is for other characters.
The Transformers Film Series gives us NEST. Unfortunately, there are conflicting explanations for what the acronym stands for - it's either Networked Elements: Supporters and Transformers, Nonbiological Extraterrestrial Species Treaty, or Nonbiological Extraterrestrial Species Team, depending on the source.
Confusing, especially since there's a real-life NEST: Nuclear Emergency Support Team.
One that's easy to overlook but obvious in retrospect, L.A. Confidential has a character, Pierce Moorehouse Patchett. Any guesses what his covert occupation was?
Upped To Eleven as pretty much every single main character with Pixar's WALL•E (Waste Allocation Load Lifter · Earth Class) has one(i.e. Extraterrestrial Vegetation Evaluator, and the Microbe-Obliterator).
From Blue Thunder, JAFO (Just Another Fucking Observer), used to refer to the chain of observers that Frank Murphy is said to go through because of his behavior. The viewer isn't made aware of the expansion until after Lymangood gets killed.
In Kiss Of Death, Little Junior claims to have an acronym for himself: B.A.D. for "Balls, Attitude, Determination". He suggests Jimmy Kilmartin (who's secretly informing on him) get one too - since he's spent most of the film as the Butt Monkey, Jimmy gives the snarky suggestion of "F.A.B." for "Fucked at birth". What seems like just a comic moment turns out to be important later, when Jimmy finds his missing young daughter... with "BAD" written on her forehead.
Batman: The Movie: Catwoman masqueraded as a writer from the Moscow Bugle named Kitayna Ireyna Tatanya Kerenska Alisoff...but suggested that Bruce call her KITKA for short. He even commented that it was a charming acronym.
In the 1981 film Looker, the device used to kill the commercial actresses is called L.O.O.K.E.R., for Light Occular-Oriented Kinetic Emotive Responses.
In the first Madagascar, Alex and Marty are reuniting on the titular island in slow-motion, and Alex slowly turns angry as he runs towards Marty (as he is why they got stranded on the island in the first place). When Marty realises this he turns the other way (still in slow motion) and yells "Oh, SugarHoneyIcedTea!"
Pacific Rim: "Chasing the RABIT", or Random Access Brain Impulse Triggers.
Pump Up The Volume: In an effort to shut down Christian Slater's guerrilla radio broadcasts, the school board and the police created a fake student outreach program to draw his attention. The program was named BIONIC: "Believe It Or Not, ICare!".
The title of S.I.C.K. Serial Insane Clown Killer. Phrasing it that way for the sake of a catchy acronym induces a bit of Ambiguous Syntax - It's a movie about an insane, serial-killing clown, not a serial killer who only targets insane clowns.
G Saviour: The nation that replaces the Earth Federation is CONSENT, or Congress of Settlement Nations.
The in-universe books written by Guru Pitka in The Love Guru fit this:
Be Loving and Open with My Emotions (which he pronounced as "bloum")
The 2008 remake of The Day the Earth Stood Still turned "Gort" into an acronym by the military, which stands for "Genetically Organized Robotic Technology". We're supposed to accept that a robot can have genes. Even one of the characters thinks that the acronym is ridiculous.