NGO Superpower

""...its influence felt on every planet from the Core Worlds to the Outer Rim. Black Sun has existed for hundreds of years, and embedded itself in the very fiber of the galaxy. The resources at its disposal are almost limitless. The soldiers under its command number in the tens of thousands. The ignorant even call it the most powerful force in the known universe.""

- Darth Sidious on the Black Sun Syndicate, Star Wars: Darth Maul

This is a Non-Governmental Organization Superpower -- an organization which is on the same power tier as the most powerful nations and yet is not itself a nation.

In fiction, we often see terrorist groups and various anti-state groups capable of going toe to toe with a regular army of the state. They may be able to field aircraft, tanks, even battleships... almost as if they had billions in tax revenue and massive installed infrastructure themselves. On occasion, these groups are shown fighting battles against modern Great Powers like USA, Russia, the EU, China, or India.

NGO Superpowers usually hold a Privately-Owned Society, and Mega Corp can be a subtrope. The Church can be this especially if Catholic and in a medieval society. An Ancient Conspiracy may be funding it. They can run the gamut from only striking nation-states when provoked to outright initiating large-scale conventional warfare and land grabs. May also be Private Military Contractors. United Nations Is a Super Power is a specific subtrope involving the UN.

Often overlaps with Nebulous Evil Organisation. Compare to Fiction 500. Contrast with NGO. State Sec is similar, only governmental. May have an Omniscient Council of Vagueness

Anime & Manga

 * The Walhaiksong can rival Zahard's government in strength and influence, especially since two of the strongest active residents, Urek Mazino and Backryung are it's founders and leaders, but they are on good terms with both the government as well as the terrorist group F.U.G.
 * Gundam 00 has the Celestial Being, which has the resources and infrastructure to build and deploy a mothership that holds its own against the space fleets of allied nations possessing orbital elevators. There is also the PMC Trust, a very powerful organization that essentially owns some smaller nations with their corporate power and military threat.
 * Expanded Universe explains that those orbital elevators themselves are indirectly controlled by Celestial Being and that its AI supercomputer Veda (housed in a massive starship that later serves as the flagship of all Earth forces) controls literally every piece of electronic information in the world, and is able to photoshop real-time video. The global conspiracy that includes the orbital elevators, Veda, and the GN drives sort of subvert this trope, as the nations of the world are unwittingly part of Aeolia's plan.
 * Nergal in Martian Successor Nadesico. While it constructs battleships for the government, The Nadesico is just a prototype they decided to use to rescue their personnel on Mars, recruiting a Ragtag Band of Misfits to crew.
 * The Searrs Group in Mai-HiME. Run by an Ancient Conspiracy, and able to field troops, tanks, and a Kill Sat. They even have a fleet, complete with carrier, though no helicopter or planes are ever seen. Flat What.
 * As an extra kicker, everything but the Kill Sat was used as expendable bait, implying that They Had Reserves.
 * Mithril in Full Metal Panic at first seems like this, but later novels and parts of the story reveals they're little more than a well-funded group of Private Military Contractors with a permanent UN contract. While more technologically advanced than the U.S. and the USSR, their entire 'Pacific Fleet' consists of a single (very advanced) submarine and they depend on small-scale surgical strikes to get the job done.
 * Akatsuki from Naruto. Especially obvious in the Fourth Shinobi World War. It's an alliance of all five of the major hidden villages, the superpowers, against...two people. Admittedly with a clone army and the ability to resurrect dead badass ninjas, but still.
 * Blue Cosmos in Mobile Suit Gundam SEED, which is a terrorist organization within the Earth Alliance, having great influence over the entity.
 * Mobile Suit Gundam SEED Destiny later reveals its just a catspaw to LOGOS.
 * The Hunter's Association from Hunter X Hunter. Understandable considering it's a gathering of the most powerful people on the planet.
 * SEELE (who controls NERV) in Neon Genesis Evangelion is a small organization, but since they are the only ones who know how to avoid the Endofthe World As We Know It, both the UN and the governments of sovereign countries give them pretty much anything they demand and sacrifice most of their armed forces when NERV requests it. They also control the EVAs, which could wipe out entire armies if they wanted to.
 * The terrestrial Romefeller Foundation in Gundam Wing - a cabal of rich aristocrats/industrialists who secretly plot to take over the world. They have so much clout to sponsor the Alliance's elite Specials, who were in reality a front for OZ.
 * Gundam Wing: Endless Waltz has the outer-space Barton Foundation, who funds two attempts to conquer the Earth Sphere.

Comic Books

 * HYDRA et al. in Marvel Comics. Although it started out as a governmental organization in Nazi Germany, and only became an N.G.O. after being (unsuccessfully) shut down
 * Also A.I.M., Them, and the Maggia.
 * Villainous organizations like Kobra, H.I.V.E. et al in the the DCU, but the Justice League of America and a few other super teams certainly qualify. Not to mention the Legion of Doom and, under certain leaders, LexCorp.
 * Obscurantis Order in Enki Bilal's Le sommeil du monstre (The Dormant Beast) is an extremely powerful sect created by the Big Bad to make the world less stable.
 * The Grail in Preacher (Comic Book) possesses a secret headquarters with a vast private army and many world leaders owe it their positions. At one point they are able to "persuade" a limited nuclear release against the Saint of Killers.
 * G.I. Joe: COOBRAAA! in the Marvel comics series they had their own consulate in New York City at one point.
 * Matt Fraction's Casanova has W.A.S.T.E, XSM and M.O.T.T all of whom have vast logistical resources.
 * A lot of writers seem forget this aspect of her character, often writing her simply as a hacker and information broker, but Oracle has influence and power on the scale of countries. Many heads of state personally owe her their positions, and she has access to the information and resources of almost every government agency. She has the capability of singlehandedly returning the human race to a pre-industrial society, and could hold the entire internet hostage if she chose to do so. Adding to this the fact that she can count on Superman, Batman and her own team to flex physical muscle on her behalf if she ever asked, and suddenly Barbara Gordon looms larger than a lot of the supposedly big deal people on the planet.

Fan Fic

 * Willard International Consulting from The Return. It funds archeological digs, can dictate to governments, has a huge R&D department which can produce superweapons upon demand, unlimited armoury inventory, has an army of special agents, several Cool Bases around the globe, is capable of producing new identities for anyone at a moment's notice, maintains a fleet of Black Hawk stealth helicopters and has a front of being just a government consultancy.
 * Team Rocket and Silph Co. both fall under this trope in the Pokémon fan fic The Mewtwo Project. Team Rocket is apparently able to field an entire fleet of various warships (including an aircraft carrier), helicopter gunships and apparently several hundred troops to take over an island. In turn, Silph Co. owns the entire island that Team Rocket is trying to take and they defend the island with autonomous autocannon turrets, helicopter gunships, patrol boats, Humvees, snipers and a shitload of heavily armed soldiers.
 * In Undocumented Featues, the Wedge Defense Force is not a government, but has its own space fleet, as does it arch-nemesis GENOM (which it keeps even after it stops being their nemesis).

Film
"Tony Stark: I have successfully privatized world peace. What more do you want?"
 * James Bond faced off with a number of NGO's:
 * SPECTRE had enough resources to manipulate the the superpowers going to war, conduct nuclear blackmail, have their own private army, and even create a space program located in a secret volcano base.
 * Hugo Drax also had his own personal space program, with a highly-advanced space station. Though somewhat implausible at the time, commercial space operations are not uncommon nowadays. Drax's operations were at least partially funded by selling equipment to governmental space agencies.
 * The Carver Media Group Network already had great influence due to its media prowess. But its megalomaniacal leader wanted more, so he influenced a war between China and Britain for his gambit. To help, Carver funds a small army and builds a stealth boat.
 * QUANTUM is a shadowy group with connections to several powerful businessmen and politicians. They can manipulate nations, and they have people everywhere.
 * Star Wars offers several different flavors:
 * The Sith are all over this, even when one of them is not Supreme Chancellor or Galactic Emperor.
 * Averted with the Rebel Alliance, who present themselves as a legitimate government -- in fact, the only legitimate government. For instance, Leia Organa was officially the Alliance Minister of State.
 * Jabba's crime empire and, in the Expanded Universe, Black Sun whose underworld influence is vast. The Zann Consortium in Empire At War is so powerful it could take on both the Empire and the Rebels in battle.
 * The Commerce Guilds probably used to be like this before they acquired enough power to actually be governments. The Trade Federation even has its own Senate representative.
 * The Jedi Order. Capable of fielding one of the most powerful militaries at extremely short notice, automatically given officer status in the Republic's forces, granted full law enforcement rights and immune from prosecution themselves, they none the less do not feel they answer to the Government and are keen to stress their independence in their internal affairs. Fortunately they are normally savvy enough to keep their shit in order, though Palpatine ultimate plan hinged on the Jedi order's naivety in taking this status for granted. The Jedi feel that they do serve the Republic - but not necessarily the Republic's current government.
 * The Hutt Cartel waver between this and being an actual government (pretty much an argentocracy) but when it all comes down to it they're a group of gangsters and merchants with no clear leader yet capable of fielding significant numbers of troops and warships, and controlling an area of space sometimes large enough to rival the republic.
 * The RDA from Avatar appears an example but is actually more of a subversion. Although they can construct interstellar space vehicles and manage a mining operation in another solar system, they are not a straight example as they are still reasonably limited in their power and actions, with what can only really be gained from there through corruption and secrecy - they'd still be no match for a real government in terms of military.
 * In Inception, Fischer's company is vying to become this (via de facto monopolizing the global energy market), which is what kicks off the plot.
 * Stark Enterprises seems to be one in the Marvel Cinematic Universe.

Literature

 * The Illuminati in Duumvirate has evolved from a more traditional conspiracy into one of these, but still secret. They're technologically superior, so they intend to drop The Masquerade and start ruling openly once their internal problems are settled.
 * Dale Brown books have the Night Stalkers/Scion/Sky Masters/Whatever-They're-Calling-Themselves-Now, who if not a per se superpower, nevertheless maintain air and ground commando forces capable of doing a number on proportionally much larger units from conventional militaries. They're staffed mainly by former members of and use the technology of Dreamland, which was a State Sec.
 * The Transnational/Metanational Corporations from the Red Mars Trilogy, which grow to be more powerful than actual terrestrial nations by the time of.
 * Kramer Associates from the novel For Want of a Nail. At one point they virtually control the government of the United States of Mexico (founded by American settlers fleeing after losing the Revolutionary War; the USM is a mish-mash of Mexican and American culture, extending from Alaska to Belize), before it becomes so corrupt they leave for Japanese Formosa. At which point they detonate a nuclear bomb (the only one in the entire world as of 1971) to safeguard their corporate interests. It was written by an economist.
 * In Sergey Lukyanenko's Line of Delirium, the Family is a criminal organization masquerading as a legitimate business. Their influence spreads far and wide throughout the Human Empire, and they have access to some of the best military hardware available, partly due to them employing the services of one of the best weapons designer in the Empire. In fact, they are so powerful that The Emperor himself names the Mother (basically, the female godfather) one of the confidantes in his will. Interestingly enough, the aTan Corporation, which is constantly described as an "empire within the Empire" and holds the key to immortality, has no private army of any kind. The Emperor, however, has to tread carefully with aTan, if he wants to keep his immortality.
 * Several Frontier corporations in Andrey Livadniy's The History of the Galaxy series have their own fleets, which they use to protect their worlds from pirates and rival corporations. One notable conflict involves a Corrupt Corporate Executive ambush a Confederacy of Suns fleet in order to capture two prototype ships, after he finds out that he is under investigation. His plan is to use the ships to threaten the entire Confederacy. While his fleet is no match for the full might of the Confederacy, this full might is usually unavailable given the need to protect many other worlds from pirates and the like. This fact is even mentioned in another novel, where the Confederacy leadership is worried that their fleets are spread too thin to reliable protect themselves.
 * Manpower, Incorporated of the Honor Harrington series thinks it is a superpower, but it is just a group of slavers and generic criminals that are the big fish in a small pond. The Star Kingdom of Manticore, their most frequent enemies in the main storyline and players in a much bigger pond, regard them as little more than a nuisance, a dime-a-dozen organization with delusions of grandeur.
 * Twenty Thousand Leagues Under the Sea: Captain Nemo's organization, the crew of the Nautilus: The Nautilus lets him loot enough submarine treasures to put him in Fiction 500, he can finance political insurrections like the Cretan rebellion, he claims the South Pole in his name, he destroys the ships of an unnamed Imperialistic Nation with total impunity. His crew is composed of men who have not place in earth and they have invented their own language.
 * The Mega Corps of Robert Aspirin's Cold Cash Wars are this. They take on the world and win! Because money.
 * The nameless corporation from Iain Banks' The Business at one point controlled the Roman Empire (though their puppet emperor only held onto it for a few months) and the novel largely revolves around its attempts to buy up a small third-world country so its senior executives can get diplomatic immunity. Not to avoid prosecution for crimes (in fact, the organization seems pretty ethical as corporations go); it's just that, once you've got your ten mansions and private helicopter, there isn't much left to buy except sovereign status.
 * In the supernatural world of The Dresden Files, nations of magical creatures such as Summer and Winter (fairies) or the vampire Courts maintain the peace among themselves through a treaty known as the Unseelie Accords. In addition to these nation-equivalents, organizations such as the wizards' White Council are also signatories, as are Monoc Industries, a supernaturally-owned corporation, and a select few powerful individuals such as the Archive. This effectively makes them "nations" by the terms of the supernatural realm.
 * And a few of the signatories are individuals and about as N.G.O. as you can get. Notable figures include a few dragons, a "semi-immortal shapeshifter guru" in the Ukraine, and Gentleman Johnny Marcone, the only plain ol' vanilla mortal freeholding lord, who has balls that drag to the ground when he walks.
 * Implicit in Daemon. The Private Military Contractors and other corporations leading the charge against the eponymous entity have enough power that at one point
 * The CHOAM Corporation in Dune. The power of the galactic nobility is mostly measured by how many shares of the company they own...as is only natural for a company that has a monopoly on a substance that extends lifespans and makes interstellar travel possible. Likewise, the Spacing Guild, who has a legal monopoly on interstellar travel.
 * The Foundation during the "Four Kingdoms period".

Live-Action TV
"Marshall: So, I've been looking over these contracts, and I gotta say, I think this might be a little out of my league. For one thing, it seems like if these contracts are not executed precisely, we will be at war with Portugal. Barney Stinson: Please, that's a Tuesday for me."
 * Altrucell of How I Met Your Mother.

""And we never part with money unless a more powerful nation forces us to, and there are only three of those left.""
 * Veridian Dynamics of Better Off Ted.


 * THRUSH of "The Man From U.N.C.L.E" and KAOS of Get Smart.
 * Interestingly subverted in the fact that the first episode of The Man from U.N.C.L.E. has Thrush's intended conquest of a small African country to be a huge deal, potentially changing the whole nature of the organization.
 * Massive Dynamic lurks as one of these in Fringe. In the second episode, Nina Sharp tells Olivia that the corporation is technically one of the ten biggest economic entities in the world. And given its research divisions, it could easily create an army if it so wished.
 * The Blue Sun Corporation in Firefly was implied to be one of these, though they may have simply been an arm of the totalitarian government. The series didn't last long enough to make it clear.
 * The Lucian Alliance of Stargate Verse, a galaxy-spanning criminal organization with enough resources stolen from the Goa'uld after their collapse to make them a dangerous force to even the Tau'ri, the most powerful race in at least two galaxies (though this is largely attributable to the severely limited scope of the Tau'ri space navy, which is limited to a half-dozen ships). By Stargate Universe, they are bold enough to attack Earth directly, albeit using suicide bomber cargo ships.

Tabletop Games

 * The Ashcroft Foundation of Cthulhu Tech embodies this trope. A globe-spanning, super-wealthy research institute and multinational, not only is it a pillar of the New Earth Government, but it invented many key inventions that define the age, from the D-engine to A-cells.
 * The traitor forces in Warhammer 40000. Justified in that the traitor forces do possess their own hidden arsenals, manufacturing facilities, and raid the Imperium pretty frequently for equipment, resources, and slaves. They did also start as a huge number of troops mutinying against the God-Emperor so it would make sense to have at least some equipment lying around.
 * The Adeptus Mechanicus have a complicated relationship with the rest of The Imperium of Man, having a form of quasi-independence that does not fall under the standard imperial rules, their own standing army, and practical monopoly on the trade, research and creation of technology. They also technically worship a heathen god, which is Handwaved as being 'an aspect of the Emperor' by the rest of the Imperium because standing on principle and provoking a crusade would effectively tear the Imperium apart.
 * VIPER in the Champions universe, as well as Doctor Destroyer's organization.
 * Most of the Mega Corps in Cyberpunk 2020 have private armies at their disposal, the most noteworthy being Arasaka and Militech, who basically supply corporate security and soldiers to everybody else. There have even been a few all-out Corporate Wars in the canonical setting.
 * The Hypercorps of Eclipse Phase go back and forth between this and Mega Corps. The nominally democratic Planetary Consortium (Mars and Luna) is run by them, but they also act independently, with enough resources and staff to do anything if they really wanted.
 * The Zhentarim of the Dungeons&Dragons world Forgotten Realms are officially a trade organization, but have become effectively the sole government in the area surrounding their headquarters at Zhentil Keep. They have their own private army and for a time the leader of the organization was also the highest ranking priest of Bane, one of, if not the most powerful evil gods.
 * The Harpers are a lose decentralized organization of rangers, bards, and other people who get around a lot, who keep track of the activities of dangerous evil organizations and churches. Their network of spies and informants in the Heartlands and the North is very extensive and they often warn local rulers of any threats that are too big for the agents to handle themselves in a quiet fashion. In addition, they count among their numbers many of the most powerful mages in the entire world and there is quite a number of formerly active agents in the courts and high ranking positions of many nations.
 * Most AA and all AAA-rating Mega Corps in Shadowrun outstrip governments in power (and in the case of one, Aztechnology, practically is the government of the entirety of Latin- and South America). The UN has been replaced by the Corporate Court, where the seven AAA megacorps are the equivalent of permanent security council seats.
 * Comstar in BattleTech, with its monopoly on FTL communication. It officially holds to a strict code of neutrality, and its members are banned from taking part in the politics of the successor states.

Video Games

 * Shinra Electric Power Corporation in Final Fantasy 7 started out as an arms manufacturer, discovered a fantastic new source of energy for an industrial world, and by the time the game begins, it is not only a Mega Corp, but it is also the closest thing the world seems to have to anything resembling government on more than a local scale, complete with a huge and well-provisioned military, public works, and a (defunct) space program.
 * Before the events of Command and Conquer: Tiberian Dawn, Interpol viewed the Brotherhood of Nod as just another terrorist organization, until they realized just how widespread that organization was and uncovered secret dealings between Nod and major US defense contractors. When Tiberium arrived on Earth, Nod quickly exploited the alien substance to gain the financial and military resources to challenge the Global Defense Initiative in open war, and though Nod suffers major defeats, each time it's able to come back with ever more advanced technology and greater numbers. By the third game, Tiberium Wars, the Brotherhood has grown into an actual state by offering humanitarian aid, governance and protection to the inhabitants of the Tiberium-ravaged "Yellow Zones," who consider GDI to have abandoned them in favor of the affluent, pristine "Blue Zones."
 * The GDI was this trope at some point, but it is a bit unclear when it entered it (UNGDI was explicitly reliant on Security Council funding and answered to the same during Tiberian Dawn, making it ultimately an arm of government [multiple governments, but still government]) and when it left this trope behind to be a government that just happened to have descended from the military arm of the United Nations.
 * The GLA from Command and Conquer Generals also averts this for the most part and justifies it when it occurs. They have no air or naval power at all, while their ground forces are either converted civilian vehicles or obsolete Soviet surplus. But the trope is played straight in Zero Hour when they kick out the Americans from Europe by capturing and using their own weapons against them, from attack helicopters, spy satellites, heavy tanks to their Particle Cannon.
 * The Private Military Contractors in Tom Clancy's H.A.W.X., who invade the USA. As Yahtzee of Zero Punctuation puts it, "Where were they hiding all this material? The fucking Moon?"
 * Mass Effect 2 has Cerberus, a human supremacist terrorist organization which, due to generous covert funding from major human organizations, owns multiple deep-space habitats, funds multibillion-dollar resurrection projects, builds bleeding-edge spacecraft, and decks its people out in spiffy uniforms. Subverted in that though they have absurd amounts of capital,
 * Mass Effect: Invasion ramps it Up to Eleven:
 * They pretty much abandon all subtlety in Mass Effect 3 and deploy a couple of light mechanized infantry regiments to locations they are interested in. You also encounter at least one cruiser and a fleet of shuttles supporting these troops. At first this seems like a strange jump in resources from one game to the next but its revealed that
 * In Mass Effect 2, the various mercenary organizations like the Blue Suns and Eclipse have their own private armies and navies; there's even one system in the game where you can read the history of a major revolution that involved Eclipse's private navy engaging in open war with the system's fleets. The Eclipse and Suns, while stateless, have vast holdings across the Terminus systems and fingers in criminal ventures throughout both Terminus and Citadel space. In particular, the Eclipse alone hold a major presence on the Asari world of Illium (they appear to virtually own the docks in the city where most of the action takes place); the Blood Pack have political clout in the krogan homeworld; and the Blue Suns control three whole planets. All three run a lot of the crime on Omega, including slave trading, element zero smuggling, and red sand trade.
 * The Shadow Broker also has his own personal army and an incredibly advanced warship whose sole purpose is to fly through massive lightning storms to shield its presence. He's described as "more powerful than anyone you've ever faced" by a Spectre as well, and those people don't exaggerate.
 * To a lesser extent, the Nos Astra Stock Exchange, judging from the horrified reaction of the Asari investor talking with the Volus moving his assets callously to profit on a humanitarian disaster.
 * Aria T'Loak's asari syndicate on Omega. With control of the trade capital of the Terminus Systems, a scarily good espionage net and Aria's playing everyone off against each other, Aria has Vetinari Job Security. How powerful is Aria? In Mass Effect 3, even after being, she can provide enough troops and ships to rival the fleet contributions of the entire Salarian Union.
 * The Metal Gear series features this quite often. Non-state players in the game of international espionage and secret warfare range from terrorist groups to renegade former government special forces units to PMCS to mysterious international conspiracies. Almost all of these groups have access to cutting technology- nanomachines, genetic engineering, and of course Metal Gear itself- and so are capable of military actions that threaten those of actual nation-states.
 * In Modern Warfare 2 (multiplayer-only), the Taliba- err, OpFor and Brazilian favela militias can somehow call down a wide variety of air support, from relatively small time UAV-launched missiles to stealth bombers, AC-130s and even a nuke.
 * In the first Modern Warfare, Al-Asad's OpFor qualifies. They had just taken control of Saudi Arabia Qurac and are able to field things like T-72 main battle tanks, Mig-29 fighters and Mi-8 helicopters. Granted they were supplied in part by the Ultranationalists.
 * Additionally for the series, the Ultranationalists themselves seem to be able to field the entire Russian military. They have BMPs, T-72 main battle tanks, Mig-29 fighters, Mi-24 Hind attack helicopters, BM-21 rocket artillery and more Mi-8s than God. Yet rarely do you encounter Loyalist forces more advanced than an infantry platoon.
 * The story's a bit of a hash, but the Mantel Corporation of Haze has apparently replaced the armed forces of every country in the world.
 * Armacham Technology Corporation in F.E.A.R. has no fewer than four major underground bunkers/facilities, an army of thousands of mercenaries, and the equipment and technology to create and arm a thousands-strong force of cloned supersoldiers.
 * This gets turned Up to Eleven in the sequels. In a specific example, the first levels of the DLC of F.E.A.R 2, Reborn consists of a massive battle between Armacham and Replica forces. This includes dozens of elite operatives on both sides, 5th Generation fighter jets, helicopter gunships and Powered Armor dropped from orbit. All of it--including the Replica slaughtering them--is the property of the Armacham Corporation.
 * GoldenEye: Rogue Agent has both Dr. No's and Goldfinger's criminal organisations. Both sides have access to vast numbers of soldiers, military vehicles and munitions. Goldfinger is capable of manufacturing a weapon of mass destruction, and No has enough troops and munitions to occupy Hoover dam (which he is apparently able to base in a tiny Caribbean island, and arm from a few small factories hidden in Hong Kong).
 * Various evil organizations in both superhero games Champions Online and City of Heroes, such as the aforementioned Viper and Argent in Champions Online, and Nemesis, the Council, and Arachnos in City of Heroes.
 * Ace Combat games have a distressing number of these. In the first game and Joint Assault, the enemies are nominally a terrorist group; in 2 they are rebels; in 3 and Advance they are a Mega Corp and in they are a mishmash of disgruntled former soldiers, but all feature some mix of WMDs, Airborne Aircraft Carriers/supermassive bombers and entire units of conventional forces.
 * While not explicitly stated to be so, the Gas Miners' Guild of Freelancer must be one, given that they fought the Eighty Year War with Rhineland... and won.
 * The Outcasts and Corsairs are a subversion. At first, they seem to be this trope. Then you visit Omicron Alpha or Omicron Gamma, and you find out that they are actually nation-states, with their own homeworlds and governments.
 * The MegaCorps in Tachyon the Fringe have their own private fleets. GalSpan (short for the Galactic Spanning Corporation) is the largest one, having their own sector of space. The only true government only has power in the Sol sector, enforced by Star Patrol. GalSpan's fleet includes carriers, cruisers, frigates, minelayers, fighters, bombers, etc. The Bora Mining Guilds are also not a true government, but their fleet is a match for GalSpan in brute force if not technology. However, most of these are hastily-converted cargo haulers.
 * The Backstory for Nexus the Jupiter Incident describes a war between IASA and several Mega Corps. The latter win, leaving Earth the only place where IASA has power. The most powerful of these is the Kissaki Syndicate, although this is due to them using Imported Alien Phlebotinum. Several early missions involve the Player Character in command of a corporation-owned corvette forced to fight much heavier ships of rival corporations. In fact, one of these battles involves saving a sister ship of the player's, which is flying an IASA banner and is openly attacked by two OSEC heavy corvettes.
 * The Twilight's Hammer Cult from World of Warcraft fits this. Other similar entities such as the Shadow Council and the Cult of the Damned are parts of larger organizations and often act as a State Sec for them. The Twilight Hammer is not. While it is under the control of the Old Gods, it's structure is otherwise independent from a larger entity. Despite this, Twilight has shown itself to be capable of taking on the armies of the Alliance, the Horde, the Dragonflights (with some support), the Guardians of Hyjal and the Burning Legion.
 * Morgan Industries from Sid Meier's Alpha Centauri, though it could be considered a government.
 * Any Mega Corp in Ground Control, but especially the Crayven Corporation and the Order of the New Dawn. Both have their own interstellar warships and huge armies, as well as colonies, but are not considered official governments. The sequel averts this, as the game is about two governments duking it out (well, one being Curb Stomp Battled by another).
 * In Team Fortress 2, two feuding Mega Corps, RED and BLU, each secretly control half of the world's governments. To add to the intrigue, the woman overseeing the feud is the CEO of both companies, as well as the CEO of a Weapons Supply Company...
 * The original Army of Two had the mercenary Strategy and Security Corporation, which hired the players and intended to.
 * And then the sequel introduced the mysterious 40th Day Initiative, which more or less blew the hell out of Shanghai The 40th Day Initiative evidently had literally thousands of troops, some of whom were wearing extremely heavy and advanced armour, along with tanks, jet aircraft and hundreds of cruise missiles. They evidently stood toe-to-toe with the Chinese Military and actually fought them off for several days.
 * In the Armored Core series, the world is entirely ruled by Mega Corps, with no trace of any governments.
 * In the 4-FA continuity, this is taken Up to Eleven, where before the events of the game, these Mega Corps destroyed the world's governments and took over the world in under a month using a small number of extremely advanced mechs.
 * The Umbrella Corporation has access to what must be billions in research equipment, a highly qualified scientific staff that they can dispose of without a thought, numerous installations all across the globe that they either hide from their host governments or operate with their permission and not just a private army but a private black-ops special forces group with helicopter and fighter jet support. And that is not counting The Virus that can turn people into zombies or giant clawed monsters. The movies take this even further, suggesting that the corporation has access to a powerful satellite network, stealth bombers and nuclear weapons.
 * In Culpa Innata NG Os have gotten so powerful that they disbanded the UN. That may or may not be a bad thing...
 * Earth Control of Martian Gothic Unification has literally taken over the world. The company can even punish "disloyalty to the company" with a death penalty.
 * The Kurvasz, a Hunter Guild in Solatorobo, had four battleships including the Golden Roar and used them and legions of infantry with Mini-Mecha to intimidate local governments.
 * In Jungle Strike, the Player Character (a lone helicopter pilot) takes on a drug lord with enough money to build a private army and purchase top-of-the-line aircraft and nuclear submarines.
 * The X-Universe games have many of these. Space Pirates and the space Yakuza field battleships, carriers, frigates, and fighter wings despite having no government, no taxes, and no known ship production facilities - though this may be explained by their capital ships being cobbled together from the wrecks of old ships. The MegaCorps, like the Optimized Technology And Shielding corporation, field their own capital ships, fleets of transporters, and patrol their home sectors with frigates and corvettes.
 * Treasures Of The Deep's Simon Black. At first, he seems like a pretty run-of-the-mill arms dealer/black marketeer. But as the game progresses, he manages to reveal that he has resources that are outside the bounds of all reason. Along the way, you discover he has built nuclear reactors in the Great Barrier Reef, shot down a space shuttle in orbit and sent a heavily armed recovery team to destroy it before the U.S Navy could recover it. What takes the cake are the final two missions. Simon's military capabilities are such that he can take on a U.S Navy Carrier Battlegroup and has a Seawolf-class attack sub, which in all likelihood his organization built itself.

Webcomics

 * Hereti-Corp from Sluggy Freelance. Even if you take away all their Mad Scientist gadgets, they were still able to send hundreds of heavily armed soldiers to capture Oasis.

Web Original

 * 'The Syndicate' in the Whateley Universe. It has an army of mooks, an elite cadre of trained killers, robot soldiers, cyborg warriors, dropships, you name it.

Western Animation

 * G.I. Joe: "Cooooooooooooobraaaaaaaaaaaa!"
 * And who funds these guys? Extensive Enterprises.
 * Cobra Industries in G.I. Joe: Renegades is a major military contractor and has numerous research and development facilities that the Joes need to break into. One of their subsidiaries is a Wal-Mart expy.
 * In Metalocalypse, Dethklok has a fleet of helicopters the size of jumbo jets, a bus that easily dwarfs small apartment buildings, an army of fanatically loyal roadies called the Kloketeers who have the authority to use lethal force anywhere in the world, Mordhaus (Which means "murder house" in German) which is shown being held aloft in the third season by a massive bank of rocket boosters that are active 24/7/365, and in the season two finale . The absurdity of this doesn't go unnoticed, as the band is described as the world's seventh-largest economy.
 * In Justice League, Amanda Waller outright states that the Justice League is easily the most powerful force on the planet. In an alternate universe, they took over the world after the death of their Flash.
 * In one episode of Gargoyles, Xanatos is called on for referring to an attack on his home an "invasion", since he's a private citizen, not a country. He replies that he's head of a major multinational corporation, and has more money and resources than many countries.

Real Life

 * The British East India Company once effectively ruled the entirety of the Indian sub-continent, Maharajas and princes surrendered their realms before its board of directors, it had armies and fleets in its name to "Protect the outposts of the Empire".
 * Its role in the Opium Wars (making the British Empire beat down on China so it could peddle opium there at their leisure) also lend it major supervillain cred.
 * Several other countries had these too, with roughly the same freedoms to exercise power. During the 17th century, the British company regularly got its ass kicked by the Dutch, and the actions of that company were such that the idea of locating the International Criminal Court in The Hague would have seemed ludicrous.
 * The Hanseatic League is perhaps one of the earliest examples. An alliance of merchant guilds that joined together for greater profit dominated the Baltic Sea and the North Sea for a few centuries. Also they were a loose and ill defined group they managed to force a lot of local rulers to grant them tax and toll exemptions for their trading posts and home cities. Major achievements include forcing the King of England to allow them to build an outpost in London and declaring war on Denmark.
 * Within the Holy Roman Empire, which was a confederation of several electors, dukes, and dozens of lesser princes that were united by their allegiance to the emperor, many wealthy cities were autonomous territories that did not have any lord and bowed only to the emperor himself. The cities of Hamburg, Bremen, Lübeck, and Cologne were governed by a council of merchants, which in reality meant by the Hanseatic League. For a time, Lübeck and Cologne were the largest cities of the entire empire and even today the modern federal states of Hamburg and Bremen are officially named "Free and Hanseatic City of Hamburg" and "Free Hanseatic City of Bremen", even though the organization has ceased to exist over 300 years ago.
 * No NGO could ever match the resources of even small nation states, but that does not mean they can not match them in influence. The CEOs of large energy companies have far more impact on the world stage than the president of, say, the Maldives.
 * Google. They are our primary source of online information, can control our web browsers, and now our phones; Google Electric and Google Space do not seem entirely implausible. The company went (verbally) toe-to-toe with the Chinese government in 2010 and fought it to a draw, pretty much deciding that China - the world's most populous country and thus one of their largest potential markets - wasn't worth it.
 * Not to mention that they've sued... the USA
 * Google Space might not be that far off, for they are at least influencing it: Google Lunar X-Prize.
 * Non Government Terrorist organizations have been the target of the 10 year long War On Terror, which by no means has been a tale of a string of crushing victories. The Taliban has less money than Pepsico, and yet it has fought a coalition of half a dozen major countries to a standstill.
 * The International Red Cross and Red Crescent is a peaceful example. Members displaying their symbols are protected under international law and the Geneva Conventions, and it has resources and personnel rivaling just about any nation.
 * The old United Fruit Company. Two Words - Banana Republic. When they came calling, you paid up your protection money and did as they ordered, or else...
 * The Roman Catholic Church influences the religious - and sometimes even political - beliefs of people all over the world and its leader also runs a tiny country.
 * For centuries it was more powerful than any government in Europe. Starting at around 1050, kings and emperors needed their permission to take the throne, and excommunication would have all your neighbors attacking you along with a good chunk of your nobles rebelling. Serfs often paid as much in tithe to the church as to their lord.
 * The Knights Templar were one of the most powerful organizations in Crusades-era Europe. They were the best Christian military force during the Crusades and established a financial empire that stretched across the Christian world. They were exempt from any law in Christian land, which was everywhere they operated and answered only to the Pope himself. They invented one of the earliest forms of modern banking. They had entire fleets of ships, built numerous fortresses in the Middle East and Europe and owned the whole of the island of Cyprus. However, after the Crusades, their influence waned and this came back to bite them in the ass. King Philip IV of France decided to take advantage of this by having their leaders tortured into confessing to heresy and burnt at the stake. Despite the heresy accusations, it was really so Philip could avoid having to pay a gigantic debt owed to the Templars. They were then arrested and had their assets seized. The sheer power and size of the organization has led a few to suggest they still survive as a secret society to this day.
 * The Rothschild family. With there insane amounts of wealth (one of the France based Rothchilds had 100 million more francs than the REST OF THE BANKERS OF FRANCE COMBINED) funded both sides of several wars, owned huge amounts of government bonds, declared NOBILITY, and were able to fund such actions as the Debeer diamond monopoly, and that is only the stuff we know about. How much power, businesses, or wealth the family had or has is a mystery.
 * Serco The Biggest Company You've Never Heard Of is in control of state schools, prisons and air traffic worldwide. They're also responsible for nuclear weapons in the UK along with other Military contracts.
 * The Hudson's Bay Company, in the 1600s and 1700s, effectively ruled a large part of the modern-day Canadian landmass.