The Amalgamated Regional Militias (ARM).
James Coburn played Derek Flint, an agent of Z.O.W.I.E. (Zonal Organization for World Intelligence and Espionage).
DC Comics has H.I.V.E. (Hierarchy of International Vengeance and Extermination).
from Marvel’s Agents of S.H.I.E.L.D.
It occurs to me that while you probably don’t want to trust an Empire, an Imperium is just absolutely no-questions-asked Bad News.
Hey, the Imperium of Man is basically as close as its universe gets to good guys.
Heresy to the Emperor!
The Traveller Third Imperium seems OK.
You misspelled “Tau Empire”.
Cleve Cartmill’s “Deadline,” from Astounding Science-Fiction, the story that got the FBI to investigate a leak in atomic secrets, used “Sixa” and “Seilla.”
An “Alliance” is usually the good guys in fiction, but it definitely wasn’t from the perspective of the protagonists of Firefly/Serenity.
The Dominion was unquestionably the bad guys in the later seasons of Star Trek: Deep Space Nine.
In The End of All Things, for the moment at least the last of John Scalzi’s excellent Old Man’s War books, there is a shadowy group of aliens called the Equilibrium which is clearly up to no good. One character, who is kidnapped and badly treated by them, writes, “I thought it was a stupid name. But they weren’t giving me a vote. And if they did I would probably name it ‘The League of Assholes,’ so I don’t think they would mind not having my input.”
Oscar Goldman and Col Steve Austin worked for the OSI which was the Office of Scientific Intelligence. (The Six Million Dollar Man)
What about
SMERSH- Death to Spys
Good guys or bad guys?
The Office of Strategic Intelligence was the predecessor of the CIA.
Nazi: Nationalsozialistische Deutsche Arbeiterpartei
KGB: Komitet Gosudarstvennoy Bezopasnosti
I love that one cartoon with the bumbling supervillians who called themselves The Legion Of Super Evil.
In The Destroyer series, Remo Williams is “recruited” by an organization called CURE. Although it’s always spelled out in caps, there was never a explanation of what it stood for.
In the indie comic normalman, there was a parody of SHIELD centering around “Sgt. Fluffy, Agent of SCHMUCK.” After every instance of the acronym, there’d be the usual asterisk for the standard footnote at the bottom of the panel. However, it would invariably say “Stands for nothing in particular.” Thing was, even after the first couple instances of this gag, the writer kept doing it, because he knew the readers would keep looking at the footnotes, thinking eventually an explanation of what SCHMUCK stood for would sneak in. 
LOVEMUFFIN
Trek Bad Guys are often Empires but they are also Unions (Cardassians) Hegemonies (the Gorn) and Alliances (the Ferengi).
There’s the Committee for the Liberation and Integration of Terrifying Organisms and their Rehabilitation Into Society.
Oh, yeah, Hegemonies are pretty bad, too. Peter Wiggin might have had good intentions, but he was still a monster.
Ever since 2003, I associate “coalition” with massive breaches of international law.
Not quite: Office of Strategic Services - Wikipedia
The Hanna-Barbera “Super Friends” were essentially the Justice League, though I don’t recall whether they called themselves that on the show.
While “Justice League” has a noble and somewhat powerful ring to it, “Super Friends” just sounds kind of silly.
However, their rival organization, the “Legion of Doom,” certainly weren’t screwing around when they came up with that name.
(By the way, I originally read the last word of the thread title as “appliances,” which was rather confusing. My refrigerator is evil and I’ve given it a name!)
Interesting dilemma.
On the one hand, SMERSH’s primary target was Nazi Germany.
On the other hand, by the end of his life, Stalin killed more human beings than Hitler.