The Witchkings effectively made their empire a state ruled by mages, since their magic was a racial trait, carried by the ruling overcaste. They also had lesser, baseline human wizards (who were not Witchkings proper, although sometimes mistaken for such by others) serving them as officers and officials.
Downplayed with Savondir. Their empire is a hereditary monarchy (under a non-magical dynasty), but their magical corps (basically a State Sec, including a Praetorian Guard) is nonetheless extremely powerful in their society, much like the Party in a more modern totalitarian state.
Present-day England is ruled by a highly corrupt version, with demon-summoning magicians ruling "commoners" through a mix of propaganda and old-fashioned intimidation.
And not just England, either: most of the major powers in history, including Rome and the Holy Roman Empire, have been ruled by magicians. Rarely have they been any better than the modern-day English regime, resulting in the Muggle common folk tending to rise up in revolution once a sufficient number of them develop innate immunity to magic due to its overuse by the ruling caste. A new, rising empire promptly supplants the old one, and the cycle starts all over again. The ending implies that the cycle is finally going to be broken, though whether this truly happens is left very much up in the air.
The Scar: High Cromlech is a thanatocracy ruled by the undead. But this does rather imply that those at the top use some fairly hefty necromancy to keep themselves and their undead minions alive.
Iron Council makes passing reference to a nation called "The Witchocracy", but it hasn't been explored in any great detail.
Bazil Broketail: The Masters of Padmasa, five evil wizards, rule their empire and seek to conquer the entire world. Argonath nominally has muggle rulers, but the Cunfshon witches exert strong (often unofficial) influence (such as by assassinating monarchs and heirs who prove to be troublesome). They rule the Cunfshon Isles openly and officially too.
The Belgariad: The Morindim are a nation of fractured tribes, each with a power-mad, demon-summoning, egomaniacal magician calling the shots. Complicating matters further is the fact that each magician quickly comes to detest the existence of every other magician — though at least the demon-summoning habit usually gets them eaten before they can amass too much power.
Anne Bishop's Black Jewels series features the Blood, powerful magic-users who effectively rule over the world, including the non-Blood (called landens). The Territory Queens, supported by their Courts (mostly male), control kingdom-sized areas, with the smaller areas (provinces, cities, villages, etc.) being controlled by less powerful Queens who answer to the Territory Queens. The quality of governance ranges from enlightened to vile corruption.
In The Broken Crescent the Monarch is the official ruler of the Kingdom of Man, but the College of Man is a law unto themselves, who control access to almost all resources through their magic and can overrule the Monarch at will.
Antaris in the Chanters of Tremaris series is ruled by the Chanters of Ice, in stark contrast to the rest of Tremaris, where chanters are widely downtrodden and persecuted. Antaris is also a Matriarchy, as it is difficult-to-impossible for men to sing the high Chantments of Ice. It is furthermore The Theocracy, as the magicians who run it are all priestesses of the goddess Taris.
Station is based on the strength of your furies, marking the society as magocratic even though everyone can wield furies except Tavi.
From the same series, the Canim Ritualists want to turn their society into this, but are having really bad luck at it so far largely as a result of getting stabbed in the back by the Vord.
The Courtship of Princess Leia: Dathomir is wholly ruled by different Witch clans using the Force (they believe that it's magic), with muggles (or men generally, as only female Witches exist) as their slaves or servants.
In the Craft Sequence, human societies are governed either by gods and their priests or by practitioners of the secular magic called Craft. Since "magic" and "law & economics" are more or less interchangeable concepts in this world, this state of affairs is perhaps inevitable.
The Crimson Shadow: Not only King Greensparrow but all his dukes are evil wizards.
A pair of novels by Lawrence Watt-Evans, The Cyborg and the Sorcerers and The Wizard and the War Machine, are set on an After the End planet that has many mages who rule all their countries. Yet each nation's government is different; some good, some bad, some outright incompetent.
Marion Zimmer Bradley's Darkover may also qualify as a magocracy seeing as it's ruled by a caste of psi-gifted aristocrats who practice a sort of Magitek in Towers.
Katherine Kurtz's Deryni series features a number of Deryni royal families — in fact, most royal families seem to have some Deryni blood. The Kingdom of Torenth is apparently a magocracy and the Muggle population doesn't seem to have a problem with it. On the other hand, the Kingdom of Gwynedd is a former magocracy and the Muggles had a huge problem with it.
The Empire of Mel'in in Diamond Sword, Wooden Sword is formally an imperial monarchy, but in fact, the Emperor is a puppet of the magical Orders of the Rainbow who actually call the shots.
Sourcery: The wizards of Unseen University set up a magical dictatorship. The results are not pretty. No one seems surprised, as any point in history where wizards have been in power has not ended well. In fact, it very nearly ends History. The only reason it seems to not happen anymore is a social paradigm shift — brought about by the current Archchancellor being unkillable, and because Lord Vetinari is clear that Wizards will never be in a position of power ever again — rather than by recent wizards being any nicer (although they seem to have collectively realized that harmless academic squabbling and enjoying huge dinners are far more pleasant and relaxing ways to spend their time than the old days of murdering each other for power and prestige).
Granny Weatherwax would be absolutely horrified by any suggestion that Lancre is a Magocracy since she knows better than anyone that magic isn't for ruling. Lancre is definitely ruled by King Verence II. And the witches will let him know if he's doing it wrong. Okay, King Verence is married to Queen Magrat, who is a Witch and who has been known to take control in a real emergency. But that sort of thing is understood.
Similarly, the witches themselves are no Magocracy because they don't have leaders. Among the leaders that they don't have, Granny Weatherwax is the most respected. It is even said once that the witches have no leader because she wouldn't allow it.
Most countries in Doctrine of Labyrinths seem to be run this way, ranging from more or less benevolent to downright oppressive. Melusine in particular is jointly ruled by an annemer (nonwizard) Lord Protector and the Curia, a council of the most influential wizards.
In the Dread Empire novels, the titular empire, Shinsan, is both a magocracy and a militocracy. At the very top is the monarch (a title jointly held by the twin Princes Thaumaturge as the series opens) who is always an extremely powerful sorcerer; immediately below them are the Military Mage class called the Tervola. Full-fledged Tervola serve as generals, provincial governors, and pretty much every other high-level position, while Tervola Aspirants fill out the lower officer and bureaucratic ranks. Muggles pretty much don't get to be anything but commoners, though someone who develops magical abilities is automatically elevated in status and may have a chance to join the Tervola (though making full Tervola when you're not from a traditionally Tervola family is hard — not impossible, but hard).
The White Council is composed of the most powerful one percent of magic users and nominally rules the magical human community. In reality, however, it mostly sticks to enforcing the Seven Laws of Magic on its fellow practitioners — you break one and, unless a Council Member agrees to take you on as an apprentice and the Senior Council agrees to it, you'll be tried, found guilty and executed in the space of an hour. And these are the good guys. — and, ironically, being a large and threatening presence to deter the other supernatural powers from trying to turn the world into this. Despite this, there's still a lot of politicking and a complex interplay between factions. A single Warden, a member of the combat arm/police force of the Council, is posted in each major city around the world, their remit being to help out local, weaker practitioners, make sure they behave and stamp on any monsters that get ideas. Due to their comparative power and Inspector Javert tendencies, the Wardens tend to be seen as something between an avenging angel and the grim reaper by your average practitioner. That and the fact that one of the weakest members of the Senior Council once dropped a satellite on someone's house, no one other than one of the other pre-eminent powers, like the Red Court of Vampires, wants to piss them off. However, the Laws of Magic are meant above all to restrict power, so that no wizard can become too powerful. It's explained that should they try to achieve power, they either have to do it the Muggle way or break one of the Laws. If they tried to meddle in Muggle politics, it would inevitably lead to civil war and the collapse of the Council. Therefore, they must remain neutral, at least as a body, when it comes to things like Muggle wars and politics.
The Red Court approximate this, with far more overt political influence in their heartlands of Central and South America (when Dresden obliterates them in the 12th book, about a dozen governments collapse overnight), while the White Court (who pretty much live for scheming and intrigue, to the point where it's a fundamental part of their culture) has the power to get a US Navy helicopter sent into a foreign country for an extraction at a moment's notice.
Juliet McKenna's Einarinn series features the city of Hadrumal, which is inhabited only by wizards. It is a kind of magic Athenian democracy, with a vote on an important issue decided not by the number of votes, but by the total magic power of those voting on each side.
The Elminster Series: Elminister's native city-state Athalantar becomes one after his uncle hires a number of mages to secure the throne, who then take over with him becoming a puppet monarch. Elminster is motivated to overthrow the "magelords" after one of them destroys his hometown to remove his self-exiled father as a potential threat to the throne.
The Elric Saga: While Melnibone is nominally ruled by the Emperor, in practice it can be seen as this, especially after Elric takes a powder, as the various Dragon Lords vie amongst each other for power and their own sadistic entertainment. A more literal example would be Pan Tang (also called the Sorcerer's Isle), which appears to be ruled by a council of wizards.
Though they seem mostly unconcerned with Muggle affairs unless someone offers them money or messes with one of their own, the Bondsmagi are theorized by some characters to actually run the world in secret. The author has implied that the Bondsmagi are happy to let the Muggles run their own lives... unless something pops up which threatens their own power, at which point they step in.
While not ruling the world, they do rule the city of Karthain. There is an official muggle power, and even elections every five years... which the mages influence and use as a playing field to settle political disputes by proxy since their own regulations strictly forbid them from directly antagonizing one another. That the Muggle ruler is a figurehead and that the Bondsmagi are the true power in Karthain isn't exactly common knowledge, but it isn't a big secret either.
Ghost Roads: The routewitches are ruled by a King or Queen who lives on the former highway called the Ocean Lady, which is also a Genius Loci and their goddess. They don't hold themselves apart from the rest of the world, but it's rare for anyone except ghosts and routewitches to visit the Queen's court. The monarch can't leave their court without giving up their immortality, and since routewitches draw power from distance traveled, all of them are compelled to pay tribute of some small amount of power to them.
Guardians of the Flame: The wizards of Pandathaway are really its rulers behind the scenes. Officially, their guild head Lucius is just one of its ruling council members.
There are a number of magical governments around the world, but The Ministry of Magic gets the most attention since it maintains control in the U.K., though it only rules over other magic-users. Muggles are explicitly outside their jurisdiction, and the Minister of Magic consults with the U.K.'s Prime Minister on matters which affect both — albeit in an infuriatingly high-handed fashion.
However, Albus Dumbledore and Gellert Grindewald once wanted the other kind of Magocracy: wizards ruling over Muggles. So does Voldemort, hence the conflict in the series.
New Aztectlan, "Hex City", in Gemma Files's The Hexslinger Series: the town is founded by a reincarnated Mayan goddess as a place where magicians, or "hexes", can actually live together and practice magic openly without wanting to vampirize each others' power to the point of death (as is true for magicians everywhere else in the world, in the series). Unfortunately, this freedom and opportunity come at the price of swearing an oath of fealty to the goddess which allows her to kill you or drain you dry at her whim, in addition to making you subject to intermittent human sacrifice. There are also a fair number of non-magical "smallfolk" in the city as well, and their lot is rather less pleasant.
Impractical Magic: Istima, the Six Court Academy, is both a wildly powerful Magic School and a city-state unto itself. Though all the leaders are mages, and powerful, the trope is subverted. At some point, wizards become so powerful that having a job, needing to afford food, and the approval of regular mortals means nothing to them. As such they stop teaching and abandon their important influential jobs to take the best parts of the Big Labyrinthine Building and slowly fade into history as they do incomprehensible things. No one is sure if they died, become gods, teleported away, are on multi-millennia astral projection trips, or if there are higher levels of the school. They just know that it's dangerous, booby-trapped, and anytime orders come down from a high tower that it must be obeyed.
The Land of Oz is a benevolent dictatorship ruled over by Glinda the Good Witch and Princess Ozma, a fairy. They and the Wizard of Oz are the only ones allowed to do magic in the sequels (to prevent wicked witches from ever rising again), but despite this the plot of pretty much every book starts with someone breaking this law.
The alfar of The Laundry Files are an extremely evil version, who are incapable of conceptualizing a society that isn't ruled by a single sorcerer of indomitable power, with literally everybody else either being a tamed, subordinate mage or a slave. Conquest is performed by slaying a sorcerer and adding the geas network controlling their civilization to your own. This would've posed a real problem for their Earth invasion plan, which hinged on our civilization working the exact same way, if only their invasion had an actual chance of succeeding in the first place.
In The Magicians by Lev Grossman, a Magician's Court that punishes magical criminals is mentioned a few times.
Patricia C. Wrede's books Mairelon the Magician and Magician's Ward are set in a world where magic does exist, and Wizards are so influential that the government and society bow to them. Specifically, British Parliament had to move out of its building because the Wizards already worked in it, and Wizards are automatically considered social equals of any level in society. It's never implied that the King of Britain is a wizard, but the Russian royalty certainly is.
In Brandon Sanderson's Mistborn series, the so-called Final Empire was founded as a magocracy, with the Lord Ruler bestowing allomantic powers on his most trusted servants, and these becoming the highest nobility of the new society. After a thousand years, the titular Mistborn sorcerers are spread fairly thin, with most nobles having weaker Misting powers or none at all. However, illegal interbreeding between classes has resulted in the power cropping up among the slave race here and there.
The Obsidian Trilogy: Armethalieh has nobles, merchants, and commoners, but unless you are a Mage, you're pretty much nothing. The Mages hold all of the high governmental positions, and most of the low ones, too.
A.L. Phillips's The Quest of the Unaligned is a partial example. While the nobles are nobles because of their magic, and the unaligned form the royal house because they have even more magic, peasants who happen to be born with magic are still looked down on by the nobles. On the other hand, peasant mages are still greatly respected by other peasants, to the degree that a mage is considered more important than the village headman.
Reign of the Seven Spellblades: The government of the Union is not discussed in detail but is strongly implied to be this. Mages sit so firmly at the top of the class system that non-magic expectant mothers sometimes ask mages for a spell that could make their child a Mage Born of Muggles for the socioeconomic advantages (according to the protagonists, no such spell exists). Demihumans are firmly second-class citizens, and that's if they're lucky: only a few species even legally get civil rights, although there's an ongoing movement to reform this.
The Reluctant King: Vorko and his compatriots had planned to establish one across the states of Novaria after he purges the wizards opposing him. Karadur, who had been his friend, is appalled and stops this. Supposedly, it would have been to spread magic for everyone's benefit. He would have been in charge of course and indicates he'll only really have people who he'd chosen to use magic.
In The Riftwar Cycle, the Tsurani Great Ones were above the law, literally able to give any order to just about anyone, with the only people able to override them being the Emperor or a larger group of Great Ones countermanding the previous order. Despite this, they did not actually run the government, though many dabbled in politics. Their status as being above the law ended when Mara of the Acoma demanded that they either run the government themselves (after providing evidence to the entire Empire that they could be outmaneuvered) or stop interfering with the people who were. They ultimately declined to turn the Empire into a Magocracy because they had a hard enough time just governing themselves.
In The Seventh Tower, the Chosen are a society of mages dominated by the most powerful magic users and those who have the best Spiritshadowsthough it turns out they're actually being ruled behind the scenes by Sharrakor, the most powerful Spiritshadow, who is quite free-willed. Those who don't have magic are called Underfolk and are a servant caste little better than slaves. From the same books, the Icecarls don't have a central government per se, but the closest thing to it would be the Crones, who are somewhere between priestesses, shamans, and mages.
The Silerian Trilogy: The water lords essentially rule Sileria in part due to their control over its water supplies. Even the official rulers have to give them tribute or they'll cut it off. Once the Valdani leave, their goal is absolute rule of the island.
In Skulduggery Pleasant each country has a Sanctuary. A magical government that rules sorcerers. They each have a council of elders that's led by a Grand Mage. The Irish Sanctuary has an Elaborate Underground Base hidden beneath a waxwork museum in Dublin.
The Steerswoman: Downplayed. In the Inner Lands, wizards don't have any formal political power and mostly keep to themselves, but whenever one of them starts giving orders, people know better than to defy them. This ranges from forcing people to work for them for no pay up to conscripting entire armies to fight their periodic, inexplicable wars between each other. In exchange, they may provide services such as predicting the weather and keeping dangerous animals at bay, according to each wizard's whims. Rowan hears an Outskirter derisively call Inner Landers nothing more than wizards' goats (the Outskirters being a goat-herding culture without wizards), and finds she can't really deny the comparison.
Aidandril is a city ruled by the Mother Confessor, a woman whose touch can make anyone fall so in love with them they'll do whatever they desire.
D'Hara has been ruled by the House of Rahl for centuries, with all of them being powerful wizards. It's said the Rahls will only accept an heir with the gift, something insured by their magic (though it has the side effect of also creating the Pristinely Ungifted, people who not only can't do it but are immune to most magic).
The Imperial Order is run by two magic users, Emperor Jagang and Brother Narev, despite their professed hatred for magic and those with it.
Vaskandar from Melissa Caruso's Swords and Fire trilogy is ruled by its "Witch Lords," a loose alliance of seventeen powerful mages who each wield absolute authority over their individual fiefdoms (the Conclave, the assembly of all the Witch Lords, deals with matters affecting Vaskandar as a whole, but a Witch Lord's right to control the internal workings of their domain as they see fit is considered sacrosanct). The country also has a Fantastic Caste System, with non-Witch Lord mages who are powerful enough to manifest a mage mark being treated as high nobility, non-marked mages still receiving some respect, and muggles being regarded in most domains as slightly better than dirt. It's eventually revealed that a Witch Lord's power derives from their magical bond with their territory, which is what makes them nearly immortal and so much stronger than other mages. This is also why Vaskandar is so aggressively expansionist — more land gives the Witch Lords the chance to expand their powers, and/or allows for the raising of new Witch Lords over conquered territory.
The elves in the Tinker Series by Wen Spencer have a strict caste system. At the top are the Doma, who, due to a genetic quirk, are capable of using magic from a distance. Violently subverted in the fact that the Sekasha, the Doma's personal guards and most elite warrior caste, have the right and duty to kill anyone, especially any Doma, who acts contrary to the good of the society/in a dishonorable fashion. They don't study magic beyond what they need to make it work.
In the Towers Trilogy, magical energy functions as both currency and power. Those who produce the most magic are the most wealthy and powerful citizens of their home Towers — with the exception of the Radiants, who are imprisoned and used as living batteries.
Inverted in Warbreaker—while most people in power in Hallandren are also skilled Awakeners, this is because they have used their wealth to buy the Breath needed to fuel the magic. In other words, the magic is like a fancy car or house in our world—not a source of influence, but a definite sign of it. Of course, ultimate power in Hallandren lies in the Court of Gods, who are mostly figureheads, and their priests (though said priests are often powerful Awakeners themselves).
The War Gods: The Empire of Ottovar enjoys 10,000 years of peace and prosperity founded by the greatest Wizards of all time. The Elves are actually a by-product of their work, taking hereditary warlocks and changing how they use the magical field to give up magic. The Empire was ruled by the emperor as well as the Council of Ottovar who prevented the misuse of magic and researched. Of course part of the backstory of the series is those 10,000 years ended rather badly and there's exactly one wizard left who isn't evil. Suddenly having a Magocracy is a bit of a problem when there aren't any left...
Tar Valon is governed by the Aes Sedai. Also, the Aes Sedai (especially the Blue Ajah) tend to meddle in the political affairs of the rest of the world, and many rulers willingly keep the counsel of an Aes Sedai advisor.
Also there is a largely unseen land called Shara, which is only mentioned in passing. However, in The World of Robert Jordan's the Wheel of Time, he mentions that it is secretly a Magocracy with puppet Muggle rulers. In seven-year cycles, each is killed then replaced by another monarch (for unknown reasons).
Meanwhile, Seanchan on the other side of the world is a complete inversion, where all the magic-users are enslaved by the Muggle rulers. Though part of the reason they developed such a hatred of magic users and got to where they are is that when they first got there that half of the world was ruled by magic-users who fought among themselves for power. And perhaps a Double Subversion, since not only the Empire is explicitly founded on the power of chained magic-users that are always at the rulers' disposal, but their handlers also in fact, are all latent magic users. They just choose to ignore this or don't understand the fact.
Wild Cards: While not technically wizards, the Psy Lords of Takis are a group of people ruling a world through their mastery of supernatural powers.
The Viiminian Empire in Wise Phuul is ruled by a council of elite Necromancers.
Wizard of Yurt: In the East, wizards also rule, unlike within the Western kingdoms.
In Sergey Lukyanenko and Nick Perumov's Wrong Time for Dragons, a large chunk of the living half of the Middle World is controlled by the four Elemental Clans. Most of the people living in the Clan lands are Muggles, who are ruled by mages. The rule is quite benevolent, and the mages use their Elemental Powers to ensure prosperity for their territories (e.g. the Water mages ensure that drought never strikes their farmlands, while the Earth mages ensure that their lands stay fertile and their mines productive). Each Clan is led by a council of first-rank mages, presided over by the clan leader, usually the most experienced and powerful of all. There was a more tyrannical version in this world's past, back when the Winged Masters ruled over all.
Piers Anthony's Xanth is a culture where every single person has one unique magical ability. The criteria for serving as King (or Queen) of Xanth include having a "Magician-caliber" ability.
In Scott Lynch's short story A Year and a Day in Old Theradane, the eponymous city-state is ruled by wizards in the Parliament of Strife. They spend most of their time getting into magical battles with each other which make life really hard for the citizens. One character with a small amount of magical talent mentions that members of the Parliament have youth spells that stop them from aging which allows them to take centuries to perfect their craft which in turn makes them powerful enough to be in Parliament.
Another Watt-Evans book, A Young Man Without Magic, uses this trope in a fantasy setting. Children found to have magical talent are automatically elevated to the nobility, and it's a capital crime for anyone else to practice magic. The non-magician emperor is more or less a figurehead. The government is mostly functional but corrupt; sorcerers have so much power that they can get away with openly using spells powered by human sacrifice.
, the eponymous city-state is ruled by wizards in the Parliament of Strife. They spend most of their time getting into magical battles with each other which make life really hard for the citizens. One character with a small amount of magical talent mentions that members of the Parliament have youth spells that stop them from aging which allows them to take centuries to perfect their craft which in turn makes them powerful enough to be in Parliament.