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.
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…
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.