Unified Naming System

There are the good guys, and there are the bad guys. Both groups are named. Now you would expect these names to be diverse, right?

Nope. If one name is an acronym, the other is too. If one name is one word, the other is too. If one is referred to thematically (such as by color, e.g. "the Reds"), the other's name will match it ("the Blues"). This is Unified Naming System. This seems weird but is probably the best way to express there's something between those two. The more cynical could also say that the reason for this is the author's lack of imagination.

Political parties in real life and fiction like to do this a lot too. Can be justified if both sides adopted names that were selected by a common third party.

Related to Fun with Acronyms and Theme Naming.

Comic Books

 * Probably stretching for this, but: Justice League vs Legion Of Doom
 * A better example is the Legion of Superheroes and the Legion of Supervillains.

Film

 * Our Man Flint. Z.O.W.I.E. (Zonal Organization World Intelligence Espionage) vs. GALAXY. (Or rather, evidently, just "Galaxy".)

Literature

 * From Gulliver's Travels, there's the Big-Endians and the Little-Endians.
 * Which actually refer to the reason for the conflict: how to eat eggs.

Live Action TV

 * Get Smart: CONTROL vs KAOS
 * Lancelot Link, Secret Chimp. APE (Agency to Prevent Evil) vs. CHUMP (Criminal Headquarters for Underworld Master Plan).
 * The Man from U.N.C.L.E.. UNCLE (United Network Command for Law and Enforcement) vs. THRUSH (Technological Hierarchy for the Removal of Undesirables and the Subjugation of Humanity).
 * Maybe, maybe not. The "expansion" of "THRUSH" was never used in any of the series episodes, but appears only in several Expanded Universe UNCLE novels.

Radio

 * Nebulous has K.E.N.T. and L.O.U.G.H.B.O.R.O.U.G.H. - both being named after British universities.

Tabletop Games

 * Champions: UNTIL (United Nations Tribunal on International Law) vs. VIPER (Venomous Imperial Party of the Eternal Reptile or Victory In Perpetuity through Eternal Resolve).

Video Games

 * Team Fortress 2: Builders League United vs Reliable Excavation and Demolition.
 * Grand Theft Auto: San Andreas: Grove Street Families vs. Kilo Street Ballaz vs. Varrio Los Aztecas vs. Los Santos Vagos.
 * INTERPOL vs V.I.L.E. in Where in the World is Carmen Sandiego.
 * The Advance Wars series have a double example: Orange Star, Blue Moon, Green Earth, Yellow Comet and Black Hole are named for both colours and astronomical objects.
 * U.N.I.T.Y vs H.A.R.M in No-One Lives Forever 1 & 2

Western Animation

 * Darkwing Duck: SHUSH against FOWL.
 * MASK. MASK (Mobile Armoured Strike Kommand) vs. VENOM (Vicious Evil Network Of Mayhem).

Real Life

 * Real Life example: Allies vs Axis
 * The Cold War in Real Life: U.S.A. vs. U.S.S.R. Wasn't the Cold War more West vs East and the examples below. And not as Hollywood History would have it the U.S.A. vs the U.S.S.R.
 * Another Cold War related one: Capitalism vs. Communism.
 * More Real Life: Triple Alliance vs Triple Entente.
 * NATO vs. The Warsaw Pact (which was sometimes referred to as the Warsaw Treaty Organisation (WTO).)
 * During the Chinese Civil War: Nationalists vs. Communists, sometimes also referred to respectively as KMT vs. CCP (their party initials).
 * The Russian Revolution: The Reds vs. the Whites.
 * In early Christian church history, two groups arose over what word best expressed the relationship between God the Father and Jesus Christ in their creeds: the homoousians (those who favored "of the same substance") and the homoiousians (those who favored "of similar substance"). Yet another group didn't really see the point to all this arguing and called themselves the homoians (a deliberately vague compromise best translated as "alike"). For the record, the first group ultimately got their way.

Wiki

 * SPOON vs FORKS vs KNIVES vs PLATTER.
 * I predict we will see a new contender trump them all and make PLATE. But then we'd have a Lensman Arms Race, with the creation of GLASS, TABLE, or even *gasp* KITCHEN!
 * At which time DEN, BEDROOM and ATTIC will make their appearance, followed by HOUSE (except that they're just fans of Hugh Laurie and only joined in the fight because it looked like fun).
 * Well, if they can't stand the heat...
 * Bah, they'll all be crushed to dirt once the Kombined Initialism Takeover Crusade Holistic Enforcement Network: Strike Insertion Neo-Kommando forces rise up.