They also allow a group of people called the World Nobles; one of whom, while riding around on one of his slaves, saw a woman that he liked the look of, and decided to take her as his 13th wife; and he shot the woman's fiancÚ when he objected. Mind you, that the World Nobles wear bubble helmets with oxygen tanks so that they don't have to breathe the commoners' air; and are completely above the law. In fact, their general portrayal is consistently "worse than it was before".
You can see them getting worse. Roswald was terrible, but he tried to look dignified. His children on the other hand...
And that "completely above the law" thing is worse than you think. If there is anyone that they can't shoot and has openly defied them, you know what they do? They summon an admiral, one of the World Government's Greatest Military Powers (basically their strongest individual fighters), to take care of the threat. To make it clear, the Admirals are on a threat level that makes anyone who isn't as strong as one of the commanders of the Whitebeard Pirates, or hell, close to the strength of one of the Yonkou, flee the immediate vicinity (as in, the island they're on, and probably the two nearest ones as well). Talk about Disproportionate Retribution.
The World Government has government-sanctioned pirates known as the Shichibukai, they ignore their laws as they please (such as the abolition of slavery), they try to cover up every major incident, such as a massive breakout of highly dangerous criminals, that would reflect badly on them, and support the doctrine of "Absolute Justice", which is basically just an excuse to murder criminals regardless of whoever is in the way, such as innocent civilians. Coupled with the fact that they allow the World Nobles run around and do whatever the hell they please, and that's when people begin to realize how corrupt "the world" of One Piece is, even by today's standards.
Kiddy Grade's Galactic Organization of Trade and Tariffs, or GOTT, is a branch of the Galactic Union (GU), a sort of United-Nations-like government over many of the planets and other locations that have been colonized by humankind across space. And of course, they get their share of conspiracies as well.
The U.S. Government in Heroman are turning into the secondary antagonists of the series.
Bleach: The Central 46 is the supreme governing and judicial body in Soul Society. It's made up of 46 members: 40 elders and 6 judges. They handle all laws and decisions regarding Soul Society, including punishments. Their orders are absolute, not even captains have the power or right to question a decision that's been made, even when their decisions are unjust. The organisation is housed in a building that has no public access. Even captains have no right to turn up there unless explicitly invited to do so (which almost never happens). The organisation not only governs from this building but also lives there. The building also contains the great archive of Soul Society's history.
There is an in-universe conspiracy theory that there's a shadow organisation secretly pulling the strings of the Central 46, but the story's only been willing to confirm that on one occasion Aizen destroyed the Central 46 and issued orders in its name to further his own agenda (the entire Soul Society arc was based around this). Once he'd been ousted from Soul Society, Captain-Commander Yamamoto temporarily functioned as the Central 46 until it was rebuilt. The organisation is a flawed system, a strong supporter of tradition, very inflexible once decisions have been made and functions in absolute secrecy making it almost impossible to hold them to account even when they're being unjust (which isn't uncommon). Even Yamamoto wasn't willing to defy the wishes of the Central 46, but his successor Kyouraku's very first act as Captain-Commander was to run roughshod over the Central 46's way of doing things, imposing his own style from the get-go and making it very clear that the relationship between the Central 46 and Gotei 13 Captain-Commander is going to undergo a very radical change. Not bad for someone who has a reputation for being Brilliant, but Lazy.
The government in the original V for Vendetta comic series was a metaphor for the British government under Margaret Thatcher. However, in the film version it's a metaphor for the Bush administration, particularly insofar as certain conspiracy theories are concerned.
The comic also goes out of it's way to show it was only after the far left took control and left NATO that the war happened causing the far right to gain control.
Up until Civil War, when this trope really went to town, the embodiment of this trope in the Marvel Universe was the insufferable Henry Peter Gyrich, the Avengers' official liason in the government. For a short, blissful time in the Busiek/Perez years, the job was filled by Dwayne Freeman, who actually liked the Avengers and wanted to make their lives easier. Of course Dwayne died making a heroic sacrifice to stop Kang the Conqueror, and the Avengers wound up with ol' Gyrich again.
Geoff Johns at least tried to make Gyrich more sympathetic during the "Red Zone" arc, in which he secretly works with Falcon (his old nemesis from back in the "You're going to be on the team because I say they need a Token Minority!" days) to discover the plots of the corrupt Secretary of Defense (who's actually the Red Skull in disguise). Once Johns was off the title, however, Gyrich not only went back to his old ways, he got worse.
While obviously more local than other examples here, Sin City has this in spades since one of the most powerful men in the state has a Serial Killer/Pedophile son who is allowed to run free.
The government in Zombo is basically every stereotype of the Eisenhower, Reagan, and Bush administrations turned Up to Eleven. Also, Donald Trump is President.
At the end of Cube, one character declares that the eponymous deathtrap was built by the government, but no one in the government really knows why; it just sort of organically grew out of too much red tape and "boundless human stupidity".
Shooter portrays the government as full of corruption and conspiracies. The hero, in the end, becomes an anti-government terrorist.
In David Wingrove's Chung Kuo series, the seven T'ang Lords even seriously discuss wiring the brains of the world's population (all 36 billion of them) in order to achieve total control: track anyone who is present at a riot or rebel attack for example, and send out pain signals as crowd control. Now that's state power.
Although in this case, the government is actively malicious. It's a world where government policy revolves around keeping the masses under control, silencing dissenters, and using the threat of (effectively identical) foreign governments to keep everyone quiet. So The Government is definitely the villain, but not strictly the kind of villain described in this entry.
The Ministry of Magic in the Harry Potter books, which seems to become increasingly corrupt as the series advances, reaching Putting on the Reich levels in the final book (after Voldemort took over, but still).
Actually, it doesn't become more corrupt at all. The atmosphere of the books changes in accordance with Harry's growing up. When he's a kid, he knows that a bad man killed his parents and wants him dead, but as he grows up, he realizes the politics behind everything, and that, while they may be "on his side," the Ministry of Magic is certainly not his friend.
The mysterious "them" in Nowhere Man certainly included the Government.
The Alliance in Firefly has many of the cinematic connotations of the Evil Empire, while they appear in the text more like The Federation. They appear first as a massive monolithic craft, staffed with a bit of Reich, casting a shadow over the protagonists. While much of their activity involves the enforcement of reasonable laws that the protagonists break, it's generally implied, and eventually confirmed, that they have something of a tendency to overstep their bounds. There are only a few characters ever shown on screen who could be called sinister, and indeed no more within the Alliance (blue hands) than outside of it (Niska), but patterns and dialogue would seem to suggest that it's not infrequent for the Alliance to mobilize its vast resources, which amplifies the effects of their plans. And in the end, a Well-Intentioned Extremist who does what he feels he must turns out to have been misled by problems Inherent in the System, making his personal moral sacrifice a complete waste.
Prison Break has two forms of government villains: the well-meaning police officers who are just following the rules and capturing the Fox River Eight in order to enforce the law, and the evil vice-president-turned-president's men who want to kill everybody that gets in the way of their massive conspiracy.
Recent seasons of 24 have featured terrorist conspiracies operating from within the White House - directed by the president in season 5, the vice president in season 6.
The new government in Jericho restores order via Private Military Contractors and a healthy dose of help from a major mega-corp. While there is a sinister connection between the corporation and the new government, the average person who works for the new system is usually only as obstructive as the new laws force them to be.
The short-lived spin off The Lone Gunmen had this as well, although the pilot had the protagonist's father point out that the evil was being done by a very small part and not the entire US government.
President Clark's corrupt, whitewashing, Psi-corps controlled government in Babylon 5 certainly fit this trope to a T, especially in the third and fourth seasons.
Stargate SG-1 averted this. The government, despite doing big cover ups, collaborating with aliens and shooting random people just for having snakes inside their heads are actually the good guys. But there's a rogue faction in NID and later The Trust that seeks to be an example of the trope.
JAG is largely an aversion of this trope; as the protagonists work for Uncle Sam, the creator and show runner is a veteran, and the show was supported by the Pentagon; not surprisingly the portrayal of the government at large (excluding the actions of certain individual characters), and the military justice system is overall very favorable. However the CIA (mostly through the character Clayton Webb) is often portrayed, in contrast to the benign U.S. military, as either (depending on the story) ruthless, inept and/or shortsighted.
The nightmarishly dystopian Imperium of Man from Warhammer 40,000, when it isn't killing you for your lack of faith, harboring enemies of the state, or for trying to secede, may kill you by accident. Due to the sheer scale of the bureaucracy running Holy Terra, the existence of entire planetary systems can be forgotten due to filing errors, while the processing time for distress signals means reinforcements can arrive generations after the war they were sent to fight is over. It is said that most of the Adeptus Terra spend their time cataloging and recording information centuries out of date, then archiving it in records that will never be read.
The fluff marches on. As of 5e, the Imperium is pretty good at waging war, and its bueracratic system is functional, if still unwieldy. Reinforments generally arrive within months, and Space Marines can respond within days because the bureaucracy that runs the galaxy is completely different than the one that runs the army. The 5th ed. rulebook still says that requests to the Adeptus Terra can result in reinforcements arriving centuries late due to Warp interference, being low priority due to that Hivefleet/Waaaagh/Chaos Warband one sector over, the message not arriving on time, or even simple human error. The new Imperial Guard codex has some rather dramatic bureaucratic mistakes as well, like accidentally drafting an entire planetary population. Twice. On the same planet. Then they ordered the planet punished for not responding the second time. They also ordered an entire regiment executed for desertion months after they all died heroically in battle.
Neo Arcadia from the Mega Man Zero games, which started out as a peaceful city-state where humans and robots lived in peace until it became fascist and genocidal after the death of its leader. Nearly dead, anyways, using his body as a Sealed Evil in a Can, and his lingering consciousness was one of the closest things the series has to a ghost.
In Metal Gear, The Government starts off as merely being a breeding ground for Machiavellian bastards who don't give a rat's ass about the hero or any other soldier. Later on, it turns out it's being controlled by a really bizarre Government Conspiracy (or even possibly an Ancient Conspiracy) of some sort, which the villain of the original MSX games is implied to have been fighting against.
The Corrupternment in Disgaea 4. It's not supposed to be terribly ideal in the best of times (it's the government of hell after all), but Valvatorez decides it's time they've gotten overthrown when they issue an order to exterminate the Prinnies... Not because Valvatorez especially cares for the Prinnies (nobody does), but because he promised each of them a sardine upon graduation, and he can't go about doing that if they're dead, now can he?
The government (specifically, a black ops group known as The Cadmus Project) was the major antagonist for Justice League Unlimited's second season Story Arc, which placed Superman, Mr. "Truth, Justice, and the American Way" in the difficult position of having to fight against the government of the country he loved so much. Fortunately, the head heavy of this organization, Amanda Waller, eventually realizes her main financial backer, Lex Luthor, is manipulating her to destroy the League. As a result, she becomes an ally of the superheroes, although that doesn't mean she wasn't prepared to kill them along with Luthor and herself as well in the climactic episode if they weren't able to defeat him on their own in the final battle to save the planet.