A.I.M. has a splinter group called R.A.I.D. or Radically Advanced Ideas in Destruction.
After M.O.D.O.K.'s death, A.I.M. created a more efficient female version called M.O.D.A.M. ("Mental Organism Designed for Aggressive Maneuvers")
One '70s-era Captain America story had him battling the Committee to Restore America's Principles, a thinly-veiled vesion of the Committee to RE-Elect the President (see below). Assemble the acronym yourself, and remember that "to" doesn't count...
He also fights the Underground Liberated Totally Integrated Mobile Army To Unite Mankind.
The Marvel Universe has S.H.I.E.L.D., Nick Fury's UN-backed paramilitary and intelligence organization. The acronym originally stood for Supreme Headquarters, International Espionage, Law-Enforcement Division but this was changed in the early nineties to stand for Strategic Hazard Intervention, Espionage and Logistics Directorate. Within the confines of the Ultimate Marvel Universe, Ultimate Spider-Man has admitted that he has no clue what S.H.I.E.L.D. stands for, even though he has regular encounters with them and Nick Fury.
And in the recent movies it stands for Strategic Homeland Intervention, Enforcement and Logistics Division.
In order to get even more mileage out of the acronym, S.H.I.E.L.D.'s extraterrestrial-focused counterpart was known as S.W.O.R.D., the Sentient World Observation and Response Department. Marvel UK had the British equivilent S.T.R.I.K.E., the Special Tactical Reserve for International Key Emergencies, and in the 90's Marvel novels gave the UN-backed S.H.I.E.L.D. a US-backed counterpart: S.A.F.E., the Strategic Action For Emergencies. S.A.F.E. has apparently since been replaced by H.A.T.E., the Highest Anti-Terrorism Effort.
Abigail Brand: I head the Sentient Worlds Observation and Reaction Department.
Hank McCoy: The government and their acronyms. Honestly, it's adorable.
Marvel UK later replaced S.T.R.I.K.E. with D.U.C.K., the Department of Unknown and Covert Knowledge. Who in turn were supplanted by W.H.O., the Weird Happenings Organisation, whose name tied with their being led by a Brigadier Stuart. Somewhere in the middle of all that there was also the Europe-wide S.T.O.R.M.; Special Taskforce Omega Response Mandate. (Marvel UK in the 90s was really a mess of agencies that replaced STRIKE, apparently created by different writers without much communication between them.)
There's also A.R.M.O.R., the Altered-Reality Monitoring and Operational Response, which is like S.W.O.R.D. for other dimensions rather than space.
S.H.I.E.L.D. was lampshaded in the Iron Manmovie, with several characters commenting on how unwieldy the Strategic Homeland Intervention, Enforcement, and Logistics Division's actual name was.
Of course the Homeland in the name in this incarnation was probably because it seems pretty heavily implied that S.H.I.E.L.D. in this movie is a purely American driven organization.
At least one spoof had Silly Humans In Extremely Lethal Danger
Spoofed with H.A.M.M.E.R. which after Osborn named it, hired someone to come up a meaning for it. What it stands for has yet to be revealed.
Much more darkly spoofed in Dark Reign: Zodiac, in which Zodiac quizzes a H.A.M.M.E.R. Agent on what the acronym actually stands for... and when he doesn't answer, he kills him.
"It's stitched on your colorful new uniform and you don't even know. Well, here's what blind faith will get you."
Also spoofed in the first issue of Mighty Avengers. In Tony Stark's narration, he states what S.H.I.E.L.D. stands for, and mentions that there's going to be voting on a new meaning.
The 2010 SHIELD miniseries has the Retcon that "The Shield" is an Ancient Tradition dating back to Ancient Egypt, which presumably implies the relatively recent S.H.I.E.L.D. incarnations were backronyms within the story.
Parodied in Jim Valentino's normalman which had a superspy organization dubbed S.C.H.M.U.C.K., but as the footnotes claim, the name "Stands for Nothing in Particular."
In DC Comics' Stars and S.T.R.I.P.E., the writers didn't bother to figure out what S.T.R.I.P.E. stood for. A fan suggested Special Tactics Robotic Integrated Power Enhancer, which DC adopted.
Possibly at least partially Justified by the creator of the S.T.R.I.P.E. suit being Pat Dugan, a.k.a. Stripesy, the former sidekick of the original Star-Spangled Kid. He may not have thought about what STRIPE meant either, it being a Shout Out to his hero days.
Those who didn't like Frank Miller's job with All-StarsBatman And Robin often get a sick glee out of pointing out how the title spells A.S.S.B.A.R.
Similarly, fans of Grant Morrison's All-Star Superman enjoy mentioning how much they enjoy "Grant Morrison's ASS"
All Star Squadron, a DC super-teamup comic in the 1980s (taking place during World War II), had similar acronym issues.
This was lampshaded by the Golden Age Superman in one of the first few issues, where he says that people should be careful how they abbreviate the group's name.
S.T.A.R. Labs (Itself an acronym for Scientific and Technological Advanced Research) has a device called the Ambient Nuclear Ultra Spectrograph. Lampshaded when Jimmy Olsen says that it's an overly long name and they should just use the acronym. The scientist operating it replies "You just think about that..."
The Legion of Super-Heroes character Wildfire was originally known as Energy Release Generator 1, or E.R.G.-1.
The Legion has to deal with the Revolutionary Elite Brigade to Eradicate Legion Supremacy.
In Grant Morrison's Doom Patrol issues, they battled the Men from N.O.W.H.E.R.E., agents of "normalcy" who only spoke in acronyms that spelled out "nowhere." At least it wasn't incomprehensible, like those guys who spoke only in anagrams, e.g., yelling "THIS!" when surprised.
Similarly, in Matt Fraction's Casanova, Casanova's father works for E.M.P.I.R.E. which battles W.A.S.T.E. (a reference to Pynchon's The Crying of Lot 49). It's never revealed what they actually stand for, but it's said that W.A.S.T.E. has multiple meanings.
DC Comics also has the H.I.V.E. or Hierarchy for International Vengeance and Extermination. In alternate universes where they are ''good' they are the Hierarchy for International Virtuous Empowerment.
A Krusty the Clown comic involved the titular character in a spy spoof, with the A.C.R.O.N.Y.M. suit on the first page (entirely spelled out in footnotes) setting the tone for a Running Gag.
In DC Comics' spy genre parody Codename: Knockout, the heroine's mother leads the espionage agency Global Organization for the Obliteration of Dastardliness and her father leads the criminal organization Extralegal Vendors of Iniquity and Licentiousness, and during one adventure she runs into agents of Heroic Englanders Against Villainy, Evildoing and Nastiness.
The sidekick of the revamped Fighting American was a cyborg named S.P.I.C.E. (Super Prototype Intelligent Cyborg Entity).
Top 10 has the city where everyone is a superhero, and the super-disease plaguing it is called "STORMS": Sexually Transmitted Organic Rapid Mutation Syndrome. It's a metahuman venereal disease that spreads through the city's super-prostitute population.
An early issue of DC Comics' L.E.G.I.O.N. had Strata propose L.E.G.I.O.N. as the name for the team, then spend several pages trying to figure out what it might stand for. Eventually they settled on Licensed Extra-Governmental Interstellar Operatives Network.
And when L.E.G.I.O.N. was taken over by Brainiac II's evil son, Revolutionary Elite Brigade to Eliminate L.E.G.I.O.N. Supremacy was formed.
The Chuckling Whatsit features GASH or The Goul Appreciation Society Headquarters. Although, the main character later learns that the acronym stands for The Global Association for Sabotage And Homicide.
DC Comics' Hawkman used to fight CAW, the Criminal Alliance of the World.
Several things relating to the Junior Woodchucks (specifcally, the ranking titles) are in the form of acronyms, including the title of the Don Rosa story: W.H.A.D.A.L.O.T.T.A.J.A.R.G.O.N, or When Huey And Dewey And Louie Originally Thought To Adapt Junior-Woodchuck Attitudes, Regulations, and Grandiose Organizational Nomenclature!
The Disney Comics database I.N.D.U.C.K.S. was rendered as an acronym as a shout out to the ones used by the Junior Woodchucks. Eventually they settled on the expansion: International Network of Disney Universe Comic Knowers and Sources
And of course, Rosa's signature D.U.C.K. which he likes to hide in his various stories, and stands for Dedicated to Unca Carl from Keno
Joe Carioca's recurring "villains" are ANACOZECA: Associacao NAcional dos CObradores do ZECArioca, or in English, the National Association of Joe Carioca's Debt Collectors. It cheats a lot (and thus usually isn't written with dots), but at least you can pronounce the acronym as a word.
In Twisted Toyfare Theater, the government agency created to enforce internal security by Megoville mayor George W. Bush (elected in 2005, look it up) and led by the Green Goblin is designated B.A.D.I.D.E.A., the Bureau of American Defense, Intervention, Deployment, Enforcement, and Analysis. "I think Mayor Bush's B.A.D.I.D.E.A. is a great idea!"
Of course, the first and most famous acronym in comics is the wizard Shazam's name (also Captain Marvel's magic word), which indicates Captain Marvel has the wisdom of Solomon, the strength of Hercules, the stamina of Atlas, the power of Zeus, the courage of Achilles and the speed of Mercury.
His evil counterpart, Black Adam, uses the same word to draw on the power of ancient Egyptian gods. He has the stamina of Shu, the swiftness of Heru (Horus), the strength of Amon (Amun), the wisdom of Zehuti (another name for Thoth), the power of Aton (Aten), and the courage of Mehen.
Referenced after DC Comics sued Captain Marvel's creators, Fawcett Comics, out of existence by DC itself. In the 1960s, Superman fought an antagonist named Zha-Vam, who was created by the gods Zeus, Hercules, Achilles, Vulcan, Apollo and Mercury. (Note he shares all but two of those with Shazam, but Vulcan and Apollo substituted for Solomon and Atlas.)
When Billy Batson's sister Mary became Mary Marvel, she had her own acronym; the grace of Selina, the strength of Hippolyta, the skills of Ariadne, the speed and flight of Zephyrus (a male god but let that pass), the beauty of Aurora and the wisdom of Minerva.
Captain Thunder, a Captain Ersatz version of Captain Marvel who appeared in Superman #276, had the magic word "Thunder!", which was formed by the power of a Tornado, the speed of a Hare, the bravery of the great Mohegan chief Uncas, the wisdom of Nature, the toughness of Diamond, the flight of an Eagle, and the tenacity of a Ram. He got his powers from a Native American shaman rather than an ancient wizard, understand.
Grendel, in the later arcs involving Eppy Thatcher and Orion Assante, features the corrupt Confederacy Of Police. All of their equipment says "COP" on it, in case you didn't get it the first time around.
With S.H.I.E.L.D., S.W.O.R.D., and A.R.M.O.R. temporarily out of the picture in Marvel comics, Mighty Avengers has introduced a new secret acronym organization: The Global Reactionary Agency for Mysterious Paranormal Activity. Enter Hank Pym: Agent of G.R.A.M.P.A.
The Order faced the mysterious MIB The M.A.N. from S.H.A.D.O.W. He's eventually revealed to be working for the Super Human Development and Operation organization, SHDO; apparently writing it as "SHADOW" is just an aesthetics thing. The "M.A.N." part doesn't mean or stand for anything, it's just to make him seem even more mysterious.
Notorious spanish comic book Mortadelo y Filemón has TIA, which when pronounced in Spanish sounds similar to tía (aunt), making it both an allegory to the CIA and a Shout Out to The Man From UNCLE. Its meaning is Técnicos Investigación Aeroterráquea (Aero-ground investigation technicians).
A subversion happens in the swedish comic James Hund with the supercomputer KENT (which, thanks to phone taps and a tendency to take everything serious, ends up killing hundreds by public demand). His inventor is interviewed on TV and the talk show host asks what K.E.N.T. stands for, but the inventor reveals that he actually named it "Kent" because it's a nice name and he used to have a budgie named Kent.
Classic Strontium Dog had an organisation called the Committee for Ultimate Retribution.
Marvel's super-man The Sentry had a super-computer which allowed him to decide which disasters to respond to in order to save as many lives as possible - CLOC, the Centrally Located Organic Computer, which only received this illustrious name with the second volume of the series. In the same series, the Sentry's evil twin the Void was revealed to possess COLC, the Computer for Obliterating Life Completely.
Not sure if this falls under Comics or Real Life, but, once after Hal Jordan went crazy and Kyle Rayner became the only Green Lantern, the real life organization dedicated to undoing this development was called HEAT.Hal's Emerald Advancement Team. Their website's mostly a Hal fanpage now, but it's here.
And then there's DC Comics itself. When the company first began in 1937, it was called "Detective Comics, Inc." Fans quickly began calling it "DC Comics," and eventually the company took this name officially. This has the unfortunate side effect of the company's full name being "Detective Comics Comics."
A spoof comic by Michael Kupperman has a boy encounter an old man who promises to give him powers whenever he says SKREWPA. The old man explains the word is an acronym and starts listing what it stands for, but after E, the boy points out, "Those are all porn movie titles!" The old man admits he forgot the actual words.
The Kingdom of Loathing comic mentions the Familiar Underground Community of the Kingdom. Jill lampshades it: "What a long name... weird how they never came up with a clever acronym."
Thunderbolts has F.A.C.T., the Federal Advisory Committee to Thunderbolts.
"The Fabulous Furry Freak Brothers" featured a group of rednecks known as Americans Secretly Serving Higher Order Law Enforcement Subservience. Yeah, you can figure that one out.
After being vague as possible about just what happened on Peter and MJ's wedding day in the new timeline that the One More DayCosmic Retcon caused, Marvel announced that a new storyline and sequel of sorts to One More Day would be released. As One More Day was considered to be an absoulte train wreck with the whole Peter and MJ were now never married thing and served as a vechile to do little more than break up the pairing, this was a bit of a hot button topic. The story in question was called One Moment In Time. Word Of God said it was intentional. The fandom was not amused (especially not so when the story turned out to be, if possible, even crappier than One More Day).
In Spy Boy, the heroic superspy organisation is called S.H.I.R.T.S., the Secret Headquarters International Reconnaisance, Tactics, and Spies. Its rival is S.K.I.N.S., the Supreme Killing Institute. S.H.I.R.T.S.' Japanese counterpart was M.A.N.G.A., the Middle Asian Network of Global Activities.