Exalted has a very powerful Necromancy spell, typically only used by antagonists, that functions as a One-Winged Angel transformation immediately upon what would ordinarily be their death. Its name? Birth Of Sanity's Sorrow.
GURPS Illuminati included a sidebar on an organization that called itself "TRI", which stood for Three Random Initials.
Subverted in GURPS IOU, which stands for Illuminati University. People asking what the O stands for are told they're not cleared to know.
Not to mention an entire department called C.T.H.U.L.H.U., which stands for College of Temporal Happenstance, Ultimate Lies and Historical Undertakings.
GURPS itself is the Generic Universal RolePlaying System.
Prior to release, it was referred to as the "Great Unnamed Role Playing System" in at least one of SJG's publications.
BattleTech has a couple fun acronyms, one that has been explicitly explained and one that is merely fun. Myomer Acceleration Signal Circuitry is a movement booster, while the NARC Missile Beacon has never been explained.
You missed the Target Aquisition Gear, a spotting laser for artillery and semi-guided missiles.
It's also very, very common for Inner Sphere BattleMech designs to have both a name and a more "technical" designation which is a combination of letters and numbers that more or less obviously refers directly back to the name. So you have the COMCommando series (nominally starting with the -1A model, though the first to see print was the -2D), the PXHPhoenix Hawks, the CPLTCatapults, the GRM-R-PRGrim Reapers... It's unclear which is cause and which effect or indeed whether the acronyms have any meaning other than as back-references even in universe. (The Clans, incidentally, seem to have shed the habit and simply refer to their units by name alone.)
FASA (the creator of BattleTech, among many other games) originally stood for the FreedonianAeronautics and Space Administration.
Rifts Chaos Earth has the Northern Eagle Military Alliance
In the main setting, there's a famous suit of Powered Armor called the Strategic Armored Military Assault Suit. Presumably it lets you hit like a girl.
Then there are the Artificial, Robot, Cerebellum, Housing, Intellect, Experiment number <x> Master Computers built by the Cyberworks Aerospace Network before the Great Cataclysm (and one built afterward).
Monsters And Other Childish Things has the Monster Investigation Bureau, which is tasked with capturing and studying what they call Biological Extraterrestrial Merchandise — if you don't get the second one, that more typically stands for Bug Eyed Monster.
The game S.A.V.A.G.E. = Survival And Victory After Global Extinction
GORE, or Generic Old-school Role-playing Engine
There is an Earthdawn adventure titled Terror In The Skies.
Mystara has "Elven Liberation Front" and "Free Armed Elven Resistant Youth" in Glantri — if you didn't guess yet, half of the time preoccupied with getting at each other's throats, as they come from two clans that don't get along at best.
In 1987, Milton Bradley put out a line of motorized action games called T.H.I.N.G.S. (Totally Hilarious Incredibly Neat Games of Skill). They used it in a motorized Girl Talk board game based off a Disney licensed product brand (hidden inside a crystal ball, voiced by Raven-Symone) a few years later.
The RAY in RAY gun stands for Radiation Accelerating Weaponry.
Shadowrun has S.U.R.G.E., Sudden Recessive Gene Emergence, an odd phenomena characterized by the sudden expression of recessive genes, often triggered by manastorms. This can result in anything from Little Bit Beastly, to Petting Zoo People, to Beast Man, to Plant People. The scientists still haven't figured out quite why animal traits are common. They also copied the System Identification Number from Gibson's Sprawl Trilogy.
Wisher, Theurgist, Fatalist is a meta-RPG by Jenna Moran in which the player characters use their stats of Knowledge, Insight, and Harmony to define the setting and play mechanics of a fantasy world.
In Eclipse Phase the rogue military AIs that destroyed Earth were called Tactical Information Total Awareness Networks. A decent allusion to Greek Mythology, but it does cause some confusion with the residents of Saturn's largest moon.
Some Game Masters refer to themselves as the Game Operations Director.