The (mostly) good counterpart to The Empire, generally a democracy and/or presided over by Reasonable Authority Figures, and a superstate composed of many different nations and races, inspired by the structure of the United States or the United Nations. The actual name may vary, but not by much. It is likely to have the words "Federation", "United", "Alliance" or equivalent verbiage somewhere in the official title.
In most sci-fi settings, the Federation is predominantly human (or composed of humans, Human Aliens and Rubber-Forehead Aliens), usually commands a fleet of Standard Human Spaceships, and is most likely to look the closest to Twenty Minutes into the Future when the other factions may be Crystal Spires and Togas, Organic Technology or both. Expect its Capital to be the Shining City and its citizens to wear anything butSpikes of Villainy or Putting on the Reich.
Rarely played as evil outright, but will usually suffer from sometimes-crippling red tape, and the occasional corrupt politicians and/or generals. Another common evil Federation set-up is The Federation opposing the independence of a number of colonies, whether space colonies in orbit, Mars or other planets in the system, or on entirely different systems. Even in this case, the main opposing force may be shown to be Well Intentioned Extremists and/or an example of The Revolution Will Not Be Civilized, willing to hurt innocent people to try to gain their independence, or worse, being used as a front for a truly evil Big Bad. The heroes will usually be either among the good soldiers of the Federation or neutral parties who get caught up in the war; this is especially true in anime. In this case, The Federation will be seen as the lesser of two evils. Another evil Federation setup is to make its governance an outright People's Republic of Tyranny.
If pitted against The Empire, is usually in a Cold War-like state, just recovering from a recent war, or a few international incidents from plunging into one. They often give covert aid (weapons, funds, supplies) to any resistance movements, but won't intervene directly unless they're already at war. In general, it frequently plays an America-like role in the political climate of the setting. If there's a movement to overthrow or undermine it, it's likely The Remnant.
Technically a "federation" is a loose conglomeration of states with common goals and purposes, coordinated by a central government that's independent of them all, and from which they have a certain amount of autonomy. One of the best examples of a federation is Russia: not only is its official name "Russian Federation", but most of the lands with a significant ethnic population, like Chechnya, are highly autonomous regions known as "republics". The Swiss Confederation is also an example. Likewise, the original design of the United States was a federation (hence "federal government"); many so-called "federations" in fiction are nothing of the sort. If the group acts much more like a single country than a bunch of mostly autonomous states, it's probably The Republic.
Note that a 'Confederation' is typically a conglomeration of states that are even more loosely bound than a Federation, the primary difference is that in a Confederation, the federal good is 'never' allowed to outweigh the good of the individual state. Switzerland is a modern example of a successful confederate democracy; the United Arab Emirates is an example of a confederation of absolute monarchies. In fiction, Confederations are typically portrayed as (at best) antagonistic neutrals and at worst, bad guys. This seems to be a holdover from the US civil war.
Compare and contrast The Alliance, usually a more temporary union of nations against a common enemy. Also compare the Fictional United Nations, where the overall governing body is weaker, it may contain both good and evil members, and it is much less unified (no unified military, and not treated as a single state by outsiders).
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Anime and Manga
Several in the Gundam series. The Federations are portrayed as flawed:
The Earth Federation in Mobile Suit Gundam. It does not allow citizens in space colonies to vote or have any say in politics (and it was responsible for exiling many of the colonists to space in the first place), leading to many, many independence groups forming. However, it's the "gray" in the series' Black and Gray Morality, contrasted against the Nazi-emulatingPrincipality of Zeon.
The Federation gets worse in Mobile Suit Zeta Gundam, with the Titans - A corrupt branch that is just as bad, if not worse, than Zeon and ruthlessly suppresses any opposition, including gassing a whole colony. After the Titans are purged, the Federation becomes more benevolent than before (and partly led by the heroes of the One Year War), but continues to have its ups and downs.
The Earth Sphere Unified Nation in Gundam Wing. Not to be confused with the United Earth Sphere Alliance, whose general corruption and oppression is what the Gundam pilots are fighting in the first place. In contrast, the Earth Sphere Unified Nation is one of the most benevolent and peaceful examples in the whole Gundam franchise.
The Atlantic and Eurasian Federations in Mobile Suit Gundam SEED. Though part of an alliance of Earth superstates, they're the major influences of that side. Typical for Gundam, both have negative aspects. Though allies, both powers mistrust each other. The Atlantic Federation is prejudiced against Coordinators, influenced by the Blue Cosmos terror group.
The Earth Sphere Federation from Gundam 00 is just a pawn for a tyrannical mastermind, abusing its political power against whoever opposes his reign - and do not forget his right-hand men, the A-LAWS, either. Once the A-Laws and it's masters fall, the Federation becomes much more nicer. By the time of the movie, the Federation is pretty much near Star Trek's level of benevolence.
In addition there's The Union of Solar Energy and Free Nations and the Advanced European Union (AEU). Averting the franchise trend, both groups are actually pretty nice, save for their Cold War with each other and the occasional political turmoil with it's members.
The Federation from Gundam AGE follows the Gundam pattern of not being especially benevolent to anyone who opposes them. Also, its decision to cover up a failed Mars colonization attempt rather than rescue the colonists is the reason the war is going on at all.
The Time/Space Administration Bureau from Magical Girl Lyrical Nanoha might be this, since they're shown acting very much like it. On the other hand, the only leadership we've seen or heard are admirals who do some civilian-leader-like tasks usually handled by elected officials, implying a military dictatorship. And the brains in jars, but they were a shadow government. Its all so vague they might still be this anyway, though, its just hard to tell.
The Free Planets Alliance from Legend of Galactic Heroes is an example of a Federation treated realistically: Its democratic ideals doesn't protect it from tyranny any more than the autocratic ideals of the Galactic Empire condemns it to tyranny.
Played with in Axis Powers Hetalia. The first episode of the anime shows a "world meeting" that is an obvious parody of the UN. Considering that the entire episode had the characters arguing and doing nothing, it's more of a subversion... or maybe not enough of a subversion.
The Federación de Planetas Federados (Federation of Federate Planets), a sort of parody from the Spanish comic-book Fanhunter.
The Web (no relation) in Nexus is miserably corrupt and often self-destructively stupid, but it's opposed by the Sov Empire, which is out-and-out evil. Nexus's world of Ylum tries to have as little as possible to do with either of them.
The Galactic Republic. In its last years the Republic was corrupt and eventually led to the formation of the Galactic Empire. Despite this, the Old Republic was remembered fondly as a beacon of civilization and peace.
The Confederacy of Independent Systems. Driven more by greed, they were far from benevolent.
The United Citizen's Federation of Starship Troopers is more of a People's Republic of Tyranny and The Empire than a Federation, being a highly militaristic and quasi-fascistic state seemingly run by a military hierarchy, complete with a Propaganda Machine. Civil rights are surprisingly good though, and racism and sexism seems to be almost entirely absent. Although the military itself is very poorly run, the general population seems to enjoy a reasonably comfortable standard of living. However, free speech is heavily restricted: anyone speaking against the Federation gets hanged. You also only become a full citizen with voting rights after enlisting in the military, or otherwise you're considered a "civilian". Surprisingly, conscription seems to be unnecessary since people will enlist to gain full citizenship anyway.
Forbidden Planet refers to a United Planets group a few times during radio calls.
The People's Republic of Haven in Honor Harrington is a very nasty and brutal deconstruction of this trope. Haven starts out as a simple Republic that is referred to as an 'Interstellar Athens' and lived in a perpetual golden age. Then the Havenite government decided to jack up the welfare programs, which in turn causes the economy to collapse. Instead of cutting the welfare programs, the Republic instead decides to turn conquistador, conquering and looting other planets to put money in their treasury. Fast forward a hundred or so years later, Haven rules a vast interstellar empire of over two hundred star systems, and its citizens are divided into the second-class "Dolists" ruled by the first-class "Legislaturalist" hereditary political families. Then, a revolution kicks off, trying to fix the system. Unfortunately the revolution is modeled after the French Revolution, complete with a leader named Rob S. Pierre. Saying that it didn't end well would be a kind of an understatement. Of course, now that the Havenite version of the Thermidorian Reaction has occurred (Thomas Theisman and Eloise Pritchart), and with their version of Napoleon removed ahead of schedule (Citizen Admiral Clusterbomb, AKA Esther McQueen), things seem to be on track for the restored Republic of Haven. Aside from the whole resumption of war with Manticore, of course — until Victor Cachat and Anton Zilwicki turn up in Nouveau Paris with proof positive that Manticore and Haven had been manipulated into war with each other by an outside third party with plans for galactic domination. This severely annoys President Pritchart, who turns up in the Manticore System at midnight, sits down with Queen Elizabeth III, and ends up not only putting a permanent end to the war, but sealing a military alliance with Manticore. The bad guys are screwed after that, and the Republic of Haven is once and for all firmly on the side of the light.
And now with the War with the Solarian League, we seem to be heading for a retelling of a combination of the Crimean War (Britain & France allied against the Colossus of Russia) and the American Civil War.
Despite its name (and being lead by the same handful of nearly-immortal humans for centuries), the Solar Empire of the Perry Rhodan series is a voluntary alliance of Earth and alien worlds with proper civil rights.
H. Beam Piper's Terrohuman Future History features the "Terran Federation".
The Harry Potter series has the "International Confederation of Wizards", which is only really mentioned as background information. Apparently the "Supreme Mugwump" is an important position.
Inverted in Terry Brook's Shannara series, where the faction called The Federation, is actually The Empire. It did originally start as a traditional Federation between several large isolated cities, it was only later that they decided it would be better for the human race if everyone was under one rule..weather they liked it or not...and every non-Human race were either exterminated or enslaved.
The Corps Diplomatique Terrestrienne of the Retief tales serve as the Federation. Granted, the CDT is a bunch of self-serving bureaucrats more interested in protocol than actual diplomacy. But they're a benevolent supranational organization willing to help humanity and its allies.
The Terran Federation from Starship Troopers. As Rico's teacher describes, "Taxes are lower and individual freedoms are higher than at any point in human history."
Also by Robert A. Heinlein, in his Between Planets the Federation began as a benign World Government with a monopoly on nuclear weapons to ensure world peace but became an oppressive tyranny.
The Confederacy of Suns in The History of the Galaxy series, although it's dissolved after nearly a millennium due to internal strife and inherent inequality in planetary rights: only the Core worlds (those originally forming it) have full rights and fleet protection, while the Periphery has to, mostly, fend for itself. After the dissolution, each world is on its own. After a few decades, though, a previously-unknown alien race conducts a sneak attack on one of the Core colonies, cutting off interstellar communication between worlds. After the aliens are defeated, their slave races become full members of the new Confederacy of Suns. In fact, one of the novels after this deals specifically with the inability of the Confederate fleet to reliably protect all of its worlds and the measures being taken to change that. Instead of a Standard Sci-Fi Fleet (which still exists but is relegated to the Core colonies), the Periphery is protected by patroling cruiser-carriers with new type of modular hyperdrive-equipped fighters.
The series also deals heavily with the time periods prior to the formation of the Confederacy, namely the First Galactic War, in which the Earth Alliance is attempting to impose its rule on a number of Lost Colonies, who have banded together. After the thirty-year war, Earth is defeated, and the colonies (which are now industrial and scientific powerhouses) form the Confederacy.
The Human Empire in Sergey Lukyanenko's Line of Delirium is presented as having elements of this. Despite the name and The Emperor, the human planets are generally left to their own devices. One planet is mentioned to have a president, implying strong local governments. While there are empire-wide laws, they are usually quite reasonable with some exceptions (such as the "kill all clones and genetically-engineered people" one). One colony is mentioned to have been brutally destroyed when it attempted to secede, but then which country is okay with having some of its territory taken away.
The Starways Congress in the Enders Game series appears to be this, until it starts showing how corrupt it really is. Even Han Fei-Tzu, one of their most respected supporters from the planet Path, is eventually forced to admit that they the Congress is full of evil men who have done and are prepared to do unspeakable things to hold on to power. Despite this, he has supported them because, in accordance with his religion (based on Daoism), the rulers automatically have the "Mandate of Heaven". Thus, their will is the will of the gods. Even when said will is to send a fleet to forcibly evacuate a colony for refusing to turn over two of its citizens for trial, even if there are plenty of people in the Hundred Worlds who think it's unjust to force people to take a 30-year trip to be tried, as it essentially means punishing them before there's even a trial. Also, the fleet is armed with a weapon capable of destroying a planet, and the Congress is fully prepared to use it. Any attempts to reveal the truth of the fleet's real mission are declared treasonous. Anyone suspected of writing "seditious" literature is arrested and tortured for information. Hmm, no free speech, cruel and unusual punishment, heavy corruption. That doesn't sound like it's what a Federation should be like.
There's also the fear the colonies have that sending a fleet to one colony that disagrees with the Congress is setting a precedent for the Congress to use the fleet to quell any opposition in the Hundred Worlds.
In addition to the Old Republic, the Star Wars Expanded Universe adds the New Republic, and the Galactic Federation of Free Alliances (Galactic Alliance for short).
The Terran Confederation of States in the Star Carrier novels is a pretty good example of a federation in the technical sense. Earth's nation-states are still around in various forms, but they all contribute representatives to a world government that grew into the Confederation, and contribute ships and soldiers to the Confederate military. The Confederation Senate is a parliamentary system with no political parties.
This seems to be changing in Deep Space, with the Confederation insisting on more and more direct control, especially over member states' Space Navies. This comes to a head when the Confederation attempts to cease an advanced AI belonging to the USNA as a "strategic asset" and use illegal weapons in their conflict with the USNA, including a Grey Goo missile to destroy the USNA capital. This causes several other member states to secede and ally with the USNA.
Subverted in Dani and eytan Kollin's Unincorporated series with the United Human Federation which starts out democratic but evolves into the People's Republic of Tyranny. Played straight with the Outer Alliance. it's left ambiguous at the end as to whether the Alliance remains together after leaving the Solar System or breaks up as it's constituents scatter among the stars
The Culture from Iain M. Banks's Culture novels is a socialist/libertarian/anarchist variant.
Live Action TV
The United Federation of Planets in Star Trek, of course. A fairly accurate example of an actual Federation, too. While they have a strong Starfleet which combines Space Navy and Space Police functions, they seem to let member worlds largely manage their own affairs and avoid military opposition to secession.
The military opposition to secession is strongly there if there's a treaty involved. The Maquis were formed by Federation colonists in the Demilitarized Zone between Federation and Cardassian space, many of whom had their planets change hands as part of a peace treaty. One group of Indians, who explicitly don't want to be in the Federation, have their planet given away and were in the process of being removed from the Federation in one episode. Military intervention was immediately canceled, however, when said group renounced their Federation citizenship, and agreed to live peacefully alongside Cardassian colonists. It didn't end well in the sequel series.
The Earth Alliance devolves into a Space NaziEmpire under President Clark, complete with the Martian-independence subtrope. It improves after a brief civil war.
The Interstellar Alliance is still new, so it's not as powerful as the one in Star Trek. However, it could easily become that and all indicators are that it will. Even has its own fighting force in the form of the Anla'Shok aka the Rangers.
After a Time Skip to 10 years later, UEO has considerably weakened, especially after the disappearance of its titular flagship (the only submarine of its kind). In that time, a new power (of The Empire kind) has been steadily gaining power, eventually forming the Macronesian Alliance (formerly New Australia), whose aggressive policies (such as annexing nearby territories without a formal declaration) remain mostly unchecked by the weakened UEO.
The Galactic Federation in Blakes Seven is very corrupt and oppressive. It was conceived as an Alliance but became an Empire. The main villain of the series, Servalan, plans to capture the Liberator so that she can create a fleet with which to take over the Federation and restore it toits former glory.
The Peacekeepers from Farscape should, however, be considered a subversion. They were no less an empire than their enemies, the Scarrans, but they were clean and well dressed (and prettier). They were also Space Nazis. The Peacekeepers essentially run more of an hegemony/Interstellar protection racket, whereas the Scarrans are more of the conquer-and-enslave types. Ironically, the Peacekeepers' xenophobia and obsession with racial purity is probably a factor in keeping them from more directly conquering their satellite states and neighbors because that might lead to fraternization.
The Systems Commonwealth in Andromeda. It was originally the Vedran Empire prior to reforms. Somehow, humans have become the dominant race in the Commonwealth, despite being one of many races in it (and Vedrans mostly being in charge).
The Earth Empire, the Galactic Federation, and the later Human Empires in Doctor Who, despite the "empire" names, fit this trope (although, because of the multi-millennial time scales involved, how well they fit varies). In most cases, planets are controlled by local governments or corporations, while the central government is benevolent but so distant as to be useless outside of a small sphere. (It does come from the former British Empire, after all...)
The Anglo-Sino Alliance in Firefly is an malevolent version. (Though the main POV characters were part of a group that lost to the Alliance ... still, we see some things with our own eyes that would justify a response of "pragmatic and ruthless" at best).
The Twelve Colonies of Kobol in Battlestar Galactica. Depicted as being rather weaker than most Federations, as its member Colonies are permitted to be as tyrannical (read: Saggitaron) or fanatical (read: Gemenon) as they please.
This is likely because the Twelve Colonies united are said to just over 50 years old, 40 years after the end of the decade long Cylon War. It is quite likely they only came together to face the threat posed by the Cylons, and mention is made of various colonies being dominated for centuries by some of the others in the series. The first episode of the Prequel series, Caprica, seems to confirm this. As a result, the only truly powerful Colonies wide organization is the Colonial Military, resulting in the occasionally dark undertones as to the influence it had on government and harsh reactions of previous President's to civil strife.
In the original version of Battlestar Galactica, the Twelve Colonies had been united for thousands of yahrens, and the ongoing war with the Cylons had lasted for 1000 years or so when Baltar's betrayal and the naivete of the ruling council led to their defeat. The original federal union of the 12 worlds was governed by a Quorum of the Twelve, and apparently each member of that council represented a tribe, rather than a world, it just so happened that each tribe had its own world. It would probably be easier to maintain the independent nature of the members of a federation if each one had its own separate world.
A Federation of sorts forms in Stargate Atlantis comprised of the various societies the Atlantis expedition had visited in their travels. They immediately turn on Atlantis, blaming them (rightfully so to a degree) for the galaxy's current problems. The comparison to Star Trek's Federation is naturally brought up, to which Rodney dismissively replies that the Federation had ships.
One must point out however that most of the problems that the Atlantis expedition where blamed for where caused by the Ancients, not them. Sheppard went so far as to point this fact out, further stating that he and his team where just trying to clean up the mess that the Ancients blatantly refuse to take responsibility for. The judge does in fact agree with him. But quickly points out that the new Federation has no power over the Ancients, so Sheppard and his team will have to take the fall.
The Migar Alliance from Tracker. Mostly good but every planet has its criminal element.
The Tau Empire, a small but Rising Empire in the galactic east, is run by the only guys in the setting who know the definition of the word diplomacy, let their allies keep their own militaries, and treat the inhabitants of annexed territory fairly well. They're also perfectly willing to use force when asking someone nicely to join the empire fails, keep client states' armies small so they're reliant on Tau support or use their vassals' forces as auxiliaries, and maintain the setting's most centralized government, divided into a caste system rumored to be mind-controlled by the ruling Ethereal class. So depending on how cynical an observer is, the Tau can be seen as either The Republic of 40k, a proper Federation, or an Empire with good publicity.
The Imperium, despite being very much The Empire of the setting, paradoxically operates as The Federationout of pragmatism. So long as component worlds pay their tithes of resources and manpower, enforce an acceptable mutation of the Imperial Cult, and hand over any psykers to the Black Ships, the Administratum lets a planet's governor run their world as they see fit. So if you live close to Terra you'll probably be in an Orwellian nightmare, while if you live in the distant realm of Ultramar it will probably seem more like The Federation. Throw in semi-autonomous factions such as Space Marine chapter fiefdoms and the loose empire-within-an-empire of the Adeptus Mechanicus and you've got a complicated political situation.
Traveller's Third Imperium is often described as a "feudal confederation". Due to the sheer size of the interstellar empire most planets are left to govern themselves as long as they pay taxes to fund the noble-run Imperial Bureaucracy and military and obey the "no nukes, no interfering with interstellar trade" laws.
The Terran Confederation in the Intersteller Wars volume of Traveller is a strange example. Though the sympathies lie with them, they are an ambitious, expansionist and conquering state. However, on the other hand, once they do conquer places they tend to treat them well.
It is not clear whether the Vilani or the Terrans are most to be blamed for the ISW's and a mild tweaking could give the Terrans more palatable justification if it suits the GM. The first Terran expansion was in trade, settling uninhabited colonies, and contact with Vilani dissidents even in canon and conquest came later when the Terrans found how tough they were. But in any case the Terran Confederation is clearly The Federation rather then The Empire despite it's aggressive foreign policy.
The Federated Commonwealth in BattleTech. Meanwhile, the Free Worlds League, while not fitting the "good guys" vibe of the trope, is more of an actual federation, with many nigh-independent worlds and regions, and the loosest central government of the major powers.
The original Star League also counts; the major members were all left to their own affairs while still being subordinate to the Terran Hegemony. It was more like The Empire to the Periphery though.
The Seven Kingdoms in Talislanta fit this trope perfectly, the moreso in that each of the seven is populated by a (very!) different race. Not all aliens have to be from outer space.
RIFTS brings us a subversion in the Federation of Magic, North America's largest gathering of magic-user communities, and the oldest enemy of the Coalition States. Subverted in that the Federation isn't generally better than the CS, nor is it really very unified at all. The head of the so-called "True" Federation, Alistair Dunscon, is an insane, power-mad Evil Sorcerer driven by a personal vendetta against the Coalition, but not everyone in the Federation supports him or even acknowledges him as their leader. The other major factions in the divided Federation either wish to be left alone and don't seek conflict (Dweomer), or are actually just in it for convenience's sake while they pursue their own agendas (Stormspire).
The Boron are both The Federation and The Kingdom, although more the latter than the former. They qualify as The Federation on basis of being a neutral/good power, and having a democratically elected leadership (the queen is a figurehead).
The Terrans may qualify, but they might also be a subversion. They're democratic according to Word Of God, but they have strong xenophobic and paranoid tendencies.
X3: Albion Prelude puts the lie to the Argon being good guys when they blow up the Torus Aeternal, a massive space station ringing Earth's equator. They then invade Terran space with a fleet of artificially intelligent warships. The X-Encyclopedia explains it in such a way as to have it make a modicum of military sense, but it's still a case of Grey and Gray Morality.
The New California Republic (NCR) in Fallout 2 and Fallout: New Vegas is a neutral example of a Federation. On one hand they are the only major faction in the entire post-Great War America that has improved the living standards of common people, by rebuilding infrastructure such as railroads, establishing trade routes, and reorganizing the code of law. But they're also selfish and corrupt, bound by countless red tape, and a semi-police state that is willing to use all kind of dirty tricks to coerce other settlements to join them. Since the only other choices are random anarchic thugs or myopic self-entitled elitist/racist/fascist groups, the NCR's about as good as any functional post-nuclear war government can get. Aside from Lyons' Brotherhood of Steel or an independent wasteland, depending on one's preferences.
Fallout: New Vegas goes out of its way to try and paint the NCR as just as bad as the other two factions, respectively a one-man dictatorship enforced by an army of robots and a band of barbarous, misogynist, pseudo-Roman slavers. This is due to Chris Avellone's (completely founded) belief that the progress made by the NCR has undermined the post-apocalyptic feel of the series, to the extent that he added a "nuke NCR" option in the Lonesome Road DLC. He's said on his twitter account that if another Fallout comes to him, he's nuking the NCR for a clean slate in the region.
The Terran factions in StarCraft usually fit this to one degree or another, although in StarCraft it is a Confederation, which is not nearly so well-intentioned. This is even worse of a misuse then the term 'Federation' tends to be, as a confederation is supposed to have even looser central government, one that wouldn't have the authority to try to retain a region that wanted to leave. It's later succeeded by the Terran Dominion, which to all intents and purposes is effectively an autocracy and much more overt in both name and intentions.
The UCN (United Colonial Nations) in the Killzone series essentially act as the United Nations. It presides over all the Earth-held colonies in space with Earth itself as its capital.
Also, the ISA (Interplanetary Strategic Alliance), the main protagonists of Killzone, act as the UCN's "NATO" forces. Every UCN colony is allowed to have its own ISA military to defend itself in times of war, but they are all under (indirect) control of the UCN.
Parodied in Star Control II, where the player character is asked to name the new good-guy faction. One of the options is the United Federation of Worlds. Another is "The Empire of [Your Name]".
The Earth Federation (later Pangalactic Federation) in Star Ocean; since SO is significantly based on Star Trek, this is quite similar to the UFP above. Can also be a subtle subversion as well, considering some of the fluff that is provided in the background data that can be unlocked in Star Ocean III.
The Federation in Frontier, Frontier: Elite and Frontier: First Encounters. Only marginally nicer than The Empire, but still a straightforward example of the trope.
Although mentioned as early as the first game'smanual, Metroid's Galactic Federation rarely got more than a passing mention until Fusion. In Metroid Prime 3, it's presented as a fairly typical good-guy federation. The Metroid: Fusion interpretation of it is starting to subvert this trope, as their goals are becoming more ruthless and self-serving. Samus could also be seen as an enemy of this more sinister Federation following her actions in Fusion as well.
F-Zero's Galactic Space Federation is also one of the many, many similarities between the respective settings of this series and that of Metroid.
Wing Commander IV also introduces the Union of Border Worlds, which is much more of a Confederation mixed with The Alliance.
The Lycian League in Fire Emblem: Sword of Seals and its prequel, Blazing Sword, are a group of small territories, each ruled by a marquess. In Sword of Seals, they fight The Empire, but in Blazing Sword they mostly squabble amongst themselves. Some endings of Sword of Seals have the main character unifying the territories into a single kingdom.
The Citadel Council in Mass Effect sits somewhere between The Federation and The Alliance. The council is acting mostly like the United Nations Security Council, consisting of the Asari Republic, the Turian Hierarchy, the Salarian Union, and the human Systems Alliance, while the other races have observer status. While each member "country" governs itself, there are common policies regarding international trade, arms treaties, and fundamental legal rights of individuals. Citadel Space appears to cover about 60 to 80 percent of the galaxy with independent colonies being clustered in the Terminus Systems.
Most of the human species is governed by the Systems Alliance, which is the only recognized representative of humans in Citadel Space, which appears to be very close to present federations on earth. Planets mostly govern themselves, but for example the military and all diplomatic relations with other species falls under federal responsibility.
Considering that they are ALSO fighting an Imperial invasion of their frontier that is stated to be militarily superior to them and probabl vastly dwarfs the forces the Empire committed to the Gallian campaign, this is probably justified.
Escape Velocity Nova features a Federation. They're definitely not portrayed the good guys, and they seem to act like more of an Empire than a Federation. They even have their own Rebellion opposing them. The Auroran Empire is a sort of confederation, being a bunch of independent, warring houses that pass around the leadership baton.
It's something of an inversion - the Federation is corrupt, and the Empire is honor-driven to a fault. In most of the endings, the player Takes a Third Option and winds up with a stable society after uniting them.
If one reads the preambles, and pays attention to what you're told in the storylines, it seems the Federation was a Federation at least, for humans, not Telepathic Spacemen, although one more corrupt and with dirtier secrets than the common example. Then came the Bureau.... Meanwhile, Escape Velocity Override has the United Earth, who is either The Alliance, The Federation, or The Empire, depending mainly upon where you draw the line between Alliance and Federation (for instance the UE does not have a common currency, but it does have a common foreign policy and Navy), your perspective on the UE's treatment of her colony worlds (note that the vast majority of humans still live on Earth), and how deeply you are affected by/fear the Voinian Empire.
The Alliance in World of Warcraft is a fantasy example of this trope. Although it would at first glance appear to be The Alliance, the only portion of the Alliance that doesn't fit this trope right down to the letter is its lack of centralized leadership, which appears to be changing with the return of Varian Wrynn centralizing power around the humans of Stormwind. The Alliance's counterpart, the Horde, resembles a (mostly) good version of The Empire due to its centralized leadership, the Warchief commands the entire Horde, and its thirst for conquest.
The humans in Master of Orion II has democracy as their default form of government. Their "Advanced government type" turns them into The Federation. Oh, and the picture of the human leader is a bald man, just in case you missed the message.
Much like The Empire, the MMORPG Pardus plays this trope pretty straight. Mostly humans? Check. Somewhat corrupt? Check. 20 Minutes Into the Future ships? Oh yes. What makes this interesting, though, is that the Federation is comprised completely of players(along with the other 2 factions, the Empire and the Union).
The United Nations Space Command from Halo began life as a textbook example of this, but a bloody civil war that was interrupted by the Covenant means that it is currently more of a military junta.
The Alliance in Breath of Fire IV is a borderline case between The Alliance and this trope, going more towards The Federation just due to the length of time it and The Empire have been at a state of running hot- and cold-wars. Six hundred years, to be precise, with at least four de facto World Wars and armistices...and the wars have lately involved the use of nuke expys by the Alliance. And you thought the Hundred Years War was bad...
The United Earth Federation (UEF) in Supreme Commander is a subversion: despite the name, it's The Empire and a military dictatorship to boot. The Cybran Nation is a better example as a loosely unified band of culturally different "nodes" that share technology and allegiance to Doctor Brackman, the father of the Cybrans, and generally only act in unison when presented with an external threat (such as the UEF above, or the Church Militant Aeon).
The Precursors has the Democratic Union, one of the possible factions the player can work for. It's a very gray organization, which is actively colonizing a planet during the events of the game and fighting the alien natives. (However, the government of said natives isn't made of saints either, and there are groups of natives willing to work with the Democratic Union against them)
The United Federation in Sonic the Hedgehog, an human federation styled after the United States, with a president and all. Its armed forces is named G.U.N. and it primary mission is to fight back the Eggman Empire and other enemies to the federation, such as Chaos and the Black Arms. Once in conflict with Team Sonic, they're now (mostly) allies to the main characters. The United Federation also appears in the Archie Comic version, now as an ally to the Republic of Acorn and an active player in the Second Robotnik War. They were also the ones who nuked Eggman Empire's former capital city the Old Robotropolis.
The nation of Malorigan in Eien no Aselia seems to fill this role. They actually seem to be at least as decent as Rakios, but due to events going on end up your enemy anyway.
By Sword of the Stars II: Lords of Winter the Morrigi are officially head of a federation comprising the other races. While players could incorporate the other races in the first game into their empires through research, the sequel will build on this with NPC FTL-incapable races to assimilate peacefully.
Galactic Civilizations: the Terran Alliance has traits of this, and forming one from everyone present is a win condition. Something similar can also happen in larger games when the weaker or more violent races have been wiped out and all the computer players decide to Gang Up on the Human.
The Nemesite Empire in The Inexplicable Adventures of Bob! appears to be like this—highly flawed, but still generally pretty decent. Although a monarchy, it is stated to have a parliament of representatives from its subject worlds. Princess Voltuptua seems to try harder than most of the royal family to do right by her subjects.
The United Nations of Sol in Schlock Mercenary, as a semi-villainous version; it's heavily factionalised, and has an extremely untrustworthy longevity project going on in secret; knowledge of this project outside those cleared for it is ruthlessly suppressed.
British Space in the Space Arc of Arthur, King of Time and Space. Despite being a monarchy, very close to being a proper federation: Arthur likes his petty kings and subject lords to have relative autonomy, because it means less work.
Associated Space features the Terran Associated States, a fairly loose federation of petty human star empires, republics, and every other form of government that's ever been tried.
Tech Infantry has the Earth Federation, which at various times both plays this trope straight and subverts it by being oppressive and evil.
Decades of Darkness has the Russian Empire/Federation, the German Empire and the British Empire.
Open Blue has the Axifloan Coalition, a very shaky confederation whose members were hated enemies no more than 170 years before the present time, stopping only because they realized fighting was stupid. Interestingly enough, its most powerful member states include two rival empires, a Vestigial Empire, and a small but extremely powerful City-State. As of v5, three of these states have declared war on one another and seceded from the Coalition, leaving it a shell of its former self.
The Federated Commonwealth in BattleTech. Meanwhile, the Free Worlds League, while not fitting the "good guys" vibe of the trope, is more of an actual federation, with many nigh-independent worlds and regions, and the loosest central government of the major powers.
The United States of America. Some of the states that make up the United States themselves could be considered such, although most are some form of unitary state. The degree of autonomy the states get is especially interesting to many foreigners.
India. Historically, many of its component territories were independent kingdoms for over a thousand years before the coming of the East India Company. Even now the highest administrative authority in the country, the Prime Minister, has less power than most world heads of government.
The European Union is, suffice to say, a complex case, even disregarding accusations of would-be or even actual Empire, but it does have clear tendencies towards this. And a few agreements and founders vaguely hinting at or suggesting this as a future goal (again, one's mileage may vary whether this is something that actually will happen, or whether the end-result would actually be The Federation).
Right now the EU is a confederation that tries as it might to become somewhat closer. The Federationis on the other end of this scale, but whether the European Union would finally move there is an open question.
A detailed study reveals that the European Union is a "sui generis" organisation that is impossible to classify into an existing category. It lacks some elements that exist even in the loosest of Confederations (no real common diplomacy or army, no obvious Head of State), but also has many elements of a Federation (mainly the fact that the law of the Union is superior to the law of the States (Federal law breaks States' law)) and even some elements of a heavily centralized unitary State (detailed and extremely specific economic regulations relentlessly enforced by the Commission and the Court). The fact that it does not correspond to anything else that existed or exist in the world and is sometimes nearly incomprehensible is one of the reasons it is becoming increasingly unpopular among some Europeans.
The closest historical equivalent might be the United States under the Articles of Confederation, which eventually resulted in the US becoming a federation. Since Europe doesn't have a war of independence to fight, there isn't really any incentive for sudden centralisation.
The UN wants to be this. Or some people want it to be this. Or some people are afraid of it becoming this whether it wants to or not. Nowhere close, though.
Switzerland. The country's individual cantons are very autonomous, and historically were semi-autonomous subdivisions of the Holy Roman Empire.
Before we move on to the various federations of The Commonwealth Of Nations, we must mention that the Commonwealth itself is conceptually descended from the idea of an Imperial Federation: those parts of the The British Empire with "responsible government" (Canada, Australia, Newfoundland,note at the time separate from Canada New Zealand, and South Africa, plus of course the United Kingdom itself) would become a single, actual federation with an Imperial Parliament and Government at Westminster to set Imperial foreign, military, and colonial policy and regulate relations among its members, while each member would still have control over its internal affairs. This idea actually got a lot of traction, but ultimately the logistics of executing it in early 20th century conspired with events to change it into the rather more toothless Commonwealth.
Canada is a strange case. Starting off as a collection of British colonies with varying degrees of self-government and cultural autonomy, it was unified together in a process known as Confederation. However, the Dominion government had much more power than the provinces at first, due to the concerns by many Canadian authorities that giving the provinces power like the US states would lead to a civil war just like the ones the Americans had recently fought. However, a lot of successful court cases and legislation by politicians (especially one from Ontario) led to the provinces gaining far more autonomy than was originally intended. During different periods of the 20th century (such as the Trudeau era), the Federal Government gained more powers in various areas, coinciding with the development of the welfare state during that time. However, Quebec had also started moving towards more autonomy and possible sovereignty, and won many concessions. Other provinces (such as Alberta and Newfoundland) also found themselves challenging the Feds. The end result is a Federation where the Central Government has a fair amount of power in many areas (such as in criminal law and enforcement, foreign policy and national defense) but where the provinces are also given a surprising amount of autonomy in others (health care, social assistance, natural resource control etc.). This is a really good example of how, while many nations may use the terms "Federation" and "Confederation", the actual mechanisms of government can be very different from each other.
The Union of Soviet Socialist Republics. Officially united by their shared Communist ideology, unofficially united by the mere fact they were once provinces of Imperial Russia.
The creation of the Soviet Union in December 1922 was an extremely complex process that would be best characterized as a Gambit Pileup: even if most of the shards of the former Russian Empire had Bolshevik, or at least Socialist governments at the time, they all had their own interests and goals, and even in the Russia proper Stalin, Trotsky, Lenin and Bukharin all had conflicting ideas about what to do next. Everyone was scheming against everyone, but military power played a surprisingly small role in that.
Most of the member states joined willingly — their respective nationalist groups failed to seize power, and communist governments just updated their status from "provinces" to "members of a federation". However, some of the latter additions to USSR — the Baltic states (Estonia, Latvia, Lithuania) and Moldavia — were conquered by the Soviets.
The "technicality" of being a Federation was suddenly no longer a mere technicality when the republics that made up the USSR decided that—since the USSR was a Federation—they were free to leave. And they did.
The Commonwealth of Australia consists of six independent states that banded together in 1901 to form a larger administrative unit within the British Empire (New Zealand and Fiji were invited and can still join if they want.) It is a strange medium between Canada's and the USA's federations; the states have the powers of the USA's states, but almost all tax revenue goes to the Federal government- which means the states are glorified government service departments. There is still significant variation in law and custom between the states (the most obvious being the definition of a certain kind of sausage, how big and what to call certain units of beer and what code of football the word 'football' is actually referring to.)
Constitutionally, the Islamic Republic of Pakistan is this. However, because the institutions inherited from colonial days haven't had any fundamental changes in terms of relations between the provinces and the central government, it still behaves more or less like The Empire, just with Islamabad (or when the military there is in charge, Rawalpindi) replacing London.
During the 19th century, the German Federation and North German Federation both existed after the collapse of the Holy Roman Empire but before the total unification of Germany.
The Holy Roman Empire and the Empire of 1871 also had aspects of a (con)federation, being composed of different states, each with a citizenship of its own (for instance, father Mozart's father saw to it that his son Wolfgang Amadeus had the citizenship of the Imperial Free City of Augsburg even though he was born and raised in the Bishopric of Salzburg) and armies that, depending on the size of the state, were more or less autonomous. In both the Holy Roman Empire and in the one founded by Bismarck there were great differences between the political systems of the individual states, ranging from absolute monarchies to quasi-democratic republics. In the Holy Roman Empire individual states pursued their own foreign policies and often as not formed alliances with foreign powers or amongst themselves (e. g. the Union (Protestant) and the League (Catholic) in the run-up to the Thirty Years' War).
The German Empire itself was a weirder example of this trope, being a federal monarchy, with the German Emperor (who was also the King of Prussia) ruling over a nation divided into many kingdoms, duchies, and other similar states. Each of these smaller states had their own rulers (the kingdoms, like Bavaria, had their own Kings, for example) and their own parliaments, and many times had minted some of their own currency and a few larger kingdoms even had their own armies, while the empire as a whole had its own currency and legislature and a combined military force, ultimately ruling as a central government for the rest of Germany.