Three fan organizations created by Rangerphiles - that is fans of Chip 'n Dale Rescue Rangers - are: Rescue Our Animated Rangers, Rangerphiles Against Gadget Erotica, and Chipperphiles Organization Against Chip Hatred.
Super Awesome VegasMagical Outing At Night With Eric And You (pronounced Save Gas Money), used on Muggle Cast.
Avalon has this as the standard naming practice for all computer systems and most of the organizations in the setting.
When the first Matrix sequel came out there was a lot of speculation about Agent Smith being able to get into the Real World and why Neo could see the Real World as Matrix Raining Code which lead to the Matrix In AMatrix, Indefinitely theory.
In the author's notes of Fuck The Jesus Beam, readers are commonly referred to as "cunts". It later turns out that this is short for "Cool Understanding Never Terrorizing Superpeople".
In the famous TDI fanfic Total Drama Comeback, we have the Kool Kidz Klub. Pretty racist.
One Less Lonely Gurl has this in SIMS and Chimps, which is Sandy's organization. It stands for Super Intelligent Mutant Squirrels and Chimps.
Ganondorf: B.E.G.? What the heck does THAT stand for? Eggman: It's our initials, dingdong! Sonic: No, it means you beg for mercy! [high-fives Link] Kirby: It also fits because Team Z.A.P. is an acronym of initials too! Bowser: Yeah…That's still a pretty clever name…beats G.E.B., that's for sure.
Zelda: Oh yeah! We are awesome baby! Z.A.P! Amy: Z.A.P.? Zelda: It's our new group! Zelda, Amy, and Peach! I tried P.A.Z. but it didn't catch on…
The United Royal Indomitable National Equestrian forces
Strangely enough, it seems as though nobody in-universe realizes the unfortunate acronym, with the narrator only noting that it seemed excessively extravagant and longwinded. Played even more straighter when Princess Luna directly calls them by that name.
DASH-E = Direct Assault Sentry Honorguard - Eradication Class
The God Squad features an Original Character (OC) who is a capricorn... otherwise known as an Oceanic Creature (OC). The OC is refered to an OC (and his actions are attributed to his OCness) often.
This trope is a favorite of the author's. We get characters worrying that actions will damage the Functionality In Canterlot), the secret agency known as the The Bureau of Undoing Trouble from Twilight Sparkle, and certain workers in said agency being Dedicated Innovation-Centered Scientists who belong in BUTTS.
Im Horseshoes and Hand Grenades, we have METEOR which means: Machine Engine Terminal: Entity Of Rancour, highlighting the fact that Ryusei's been configured into a cyborg.
A non-canon side story in The Non-Bronyverse involves the Delegation of the Office of the Royal Knowledge Society, or D.O.R.K.S. Celestia has somehow previously failed to pick up on this over the past thousand years or so.
The Reading Rainbowverse has the Committee On United Chairs and Headrests, meant to be a group of furniture experts. There was also, briefly, the Council United to Reinstate Brown and Show Tyrants Overtly Merciful Protest.
In My Little Unicorn, Brain invents a tracking device called TERRIFIC (The Elemental Radar Receptor In Finding Interesting Characters).
In Flash Fog, we have the Society for the Prevention of Human Exploitation in the Realm of Equestria, or "SPHERE" for short. The name also conveniently uses Ambiguous Syntax to cover both situations in which humans are exploiting Equestria, and being exploited by Equestrians.
Starlight Over Detrot has the Perimeter Aegis Control Taskforce, or PACT, that is charged with protecting Detrot from Megafauna, as well as the Polite Enjoinder Against Criminal Enterprise (PEACE) cannon.
Errant Road, an on-line RPG/fanfic associated with the Errant Story webcomic, has the Offensive Chronomancy Research Abolition Protocol, a treaty restricting the study of time magic, named for what the researchers say just before the forbidden magic blows up in their faces.
In Royal Heights there's the reveal of the HEADMASTER which decodes to Highly Elaborate Academically Directed Machinery Allowing Students To Excel Reality.
In Hunting Series there's the initalism - M.H.M.I or Matrix Hunter Monitoring Interface. Without being connected to M.H.M.I you're not a offically a hunter and that can be a very bad thing.
In The Cracks That Show Gringotts sends Harry a message box for Emergency Messages for Automated Interdepartmental Letters.
A Rational Child has the Magical Academy for the Gifted, Intellectual and Cultured.
The title of the My Little Pony fanfic MANE is an acronym that reflects the plot of the story as well as being a pun on real-world nuclear doctrine. It stands for 'Mutually Assured Nuclear Extinction.'
Thousand Shinji: While they're checking weapon upgrades, Shinji grows frustrated with the number of nonsensical-sounding acronyms:
“Well, there’s the boom pistol, or rather the APHEGSRB-PV, or Pistol Variant. It was developed along with the carbine version you’re using, but as the name suggests it is smaller and has a somewhat shorter range. And then of course there is the RCPTCCW,” Misato says. “What is with all the acronyms?” Shinji asks in annoyance. “It’s a military organization, live with it,” Misato says with a shrug. Punching in a few codes in his entry plug, Shinji examines the meaning of the acronym before saying, “Rotary Chain Progressive Tooth Close Combat Weapon… you made a giant chainsaw!”
In Tournament Hilarity Harry appoints a substitute champion to take his place in the Triwizard Tournament. Said champion announces that he'll be representing the Demon's Establishment of Annihilation and Darkness.
Escribamens has the Early Magical Strength Core Undeveloped Latent Talent Evaluation.
Beautiful Destroyer Sailor Moon gets in a couple of good ones, starting with the title itself note BDSM. The one that really takes the cake though is We Are Fanatical Fans Enthusiastically Needing Sailor Senshi or W.A.F.F.E.N. S.S.. They even have armbands.