Fans! adjusted the Federal Bureau of Investigation into the Fantasmagorical Investigation Bureau, or FIB.
The secret anti-alien organization in It's Walky! is called SEMME... which does stand for something, but the author has yet to reveal what. It's pronounced like "semi", creating useful pun fuel. In one strip, part of the E on their building is blown off, prompting Walky to start calling the organization "SEMMF".
I'd think there'd be more pun fuel if it were pronounced how it looks.
The author once claimed to have forgotten what SEMME stood for (having invented it in his childhood).
The KA Mics had the Semi-Mystical Otherworldy Gates or S.M.O.G. Nothing deep about the name though, the author took the acronym from a running gag he was part of on one of Nitcentral's humor threads.
Mr. Mighty in Everyday Heroes is a member of The Society of Amazing, Valiant, and Extrememly Unselfish Superheroes ... S.A.V.E.U.S.
According to the cast page, Mr. Mighty has previously worked for the Team Hoping to Uphold Decency (THUD), the White House Advanced Personnel Protective Office (WHAPPO), the American-Mexican International Group Of Superheroes (AMIGOS), and the Group Of Official Do-Gooders United In Suppressing Evil (GOOD GUISE.).
A straighter example is this strip, where Douglas Hofstadter's autobiography reads, "I'm So Meta, Even This Acronym".
Penny Arcade gives us Gamers Against Exercise, a theoretical support group founded by Gabe who support traditional, controller-based gaming. Especially funny on a shirt.
The Perpetual Aquarium had the fish take the Comprehesive Assessment and Report of Progress, or CARP. This was lampshaded when one of the fish comments that basing a year's progress isn't CARP, it's C——, and, when interrupted, comments that he likes anagrams.
The name was suggested by a reader after the writer decided he had to call it something so he might as well call it DAVE.
The Trustworthy Room test from Tower of God requires to gather rooms and teammates, though with a high risk of losing ones room. So Ja Wangnan and Nia decide to do it the gentlemanly way: Operation S.I.R., Stay In the Room.
In the Jet DreamRemix Comic, the T-Girls represent NATO's Joint Elite Team, Division of Raiding-Expert Aeronautical Maidens (J.E.T. D.R.E.A.M., or usually just "Jet Dream.") Their "little sister" team is Junior Echelon, Teen T-Girls, Elle-Boys, and Esprit-Girls (Natural!), or J.E.T. T.E.E.N. Both organizations must deal with the sinister schemes of Zoned Extortion and Removal, Occidental (Z.E.R.O.).
Erfworld has Lord Stanley the Tool's elite hobgobwin knights, the Knights In Stanley's Service. They are, of course, a reference to the band KISS; their "war paint" is the makeup KISS wears onstage, and their name is a reference to the old moral panic-driven legend that KISS stood for "Knights In Satan's Service" (which it didn't).
The GIGAHERTZ, or Gizmonic Institute Graphical Automated Hyper-Enhancement of Reality through Teleportation and, uh... Zoom, from The Way of the Metagamer.
Responded to with the Clayton Forrester Volumetrically Displayed Entertainment and World-Taking Over Device, or, uh... CFVDEWTOD (khfhvhdootodd?) for short.
And then later, when Caliborn takes over the narritive and is retelling the story, he can't remember the name of Dave's planet, and so invents his own. What does he call it? Land of Someone's Handicraft I Took (LOSHIT).
The Crossover Wars had their DRACO (Dimensional Reality Arcane Crossover Organizer)
Violet: And you're U.N.I.T.Y. Unity: Yep! Violet: The Upgradeable Necrotic Independent... what? Unity: We don't talk about my acronym. Violet: Sorry, did I touch a nerve? Unity: Well, you know. People died and stuff. Violet: People died... because of your acronym. Unity: The committee meetings, man! It was law of the jungle!
In a later arc, we meet G.O.D.O.T., an AI whose primary function is a military-grade backronym generator. It turns out G.O.D.O.T. went mad trying to work out what U.N.I.T.Y. could stand for, which is presumably the point at which people died.