In Ooku, the retreat of Tokugawa Japan from the rest of the world is given a different reasoning. A disease is killing off a many of the men and the privy council ruling in the name of the dead shogun fears the outside world moving in for easy pickings.
Ashitaka's Emishi tribe in Princess Mononoke, though as the last surviving pocket of an ethnic group thought to have been wiped out centuries ago, their strictly-enforced isolationism isn't without reason.
Record of Lodoss War: The Forest of No Return is the home of the elves of Lodoss. To ward off any visitors, the forest changes shape and traps them inside with the intent that they die trying to escape. While most elves try to stay, several have left to see the world for themselves, namely Deedlit and Pirotess.
Rune Soldier Louie: After being captured by Louie, Celecia pretends to guide him and his friends back to her village, and walks them straight into a trap set by her people. Though she does speak on their behalf, while they're there, to prevent them from being executed for trespassing into their forest.
The kithkin, a race of halflings in Magic: The Gathering's Shadowmoor setting, are paranoid and xenophobic in the extreme, holing themselves up in walled castles and brandishing Torches and Pitchforks against anyone who isn't just like them.
Pictured above is "Secret Village of the Spellcasters".
Themiscyra, a.k.a. Paradise Island (Hidden Amazon Village) in The DCU.
Attilan (Hidden Inhuman Village) in the Marvel Universe, which had the extra fun of getting moved about to stay hidden ? it began as a faux Atlantis in the Backstory which later became The Shangri-La, and then alternated between that role and being placed on the moon.
Sorrow's End in ElfQuest is an oasis in the middle of an inhospitable desert, established in an attempt to escape human persecution. The inhabitants aren't exactly hostile to outsiders, at least those of their own species, but they do end up having to defend it against hostile elves and later humans. After thousands of years the village eventually falls. Although the invaders are defeated and most of the villagers survive, it's a pyrrhic victory because the village is destroyed and the survivors have to take refuge in abandoned troll caverns beneath the desert, before eventually being found and relocated by the other elves in the flying Palace of the High Ones.
Blue Mountain may have been written as a darker counterpart to Sorrow's End - what if isolation goes far too far. To get it out of the way: There are exactly five known survivors. One of them, Winnowill, had been some kind of insane probably for millennia, directly caused by their isolation, since it made her healing magic superfluous and "fester". She became the Big Bad of several subseries, also creating some nasty monsters on the side. One of the other survivors, Door, was her apprentice, or driven mad by her somehow, and became a tyrannical god-king, Big Bad of Forevergreen. Then there is her son, who in all likelihood would not have been born if she'd been sane. Imagining ElfQuest without Two-Edge engineering a war to figure out who he is is left as exercise to people who know the series.
Daxam, in the DCU, is a hidden elf planet. Its inhabitants are incredibly racist and xenophobic, even after their lives are saved by the Green Lantern Corps.
Abilon in the pre-soft reboot Archie Comics' Sonic the Hedgehog was a city filled with Echidnas, hidden away from the rest of the world and believed that they didn't need to help Mobius. This came back and bit them in the ass thanks to a Chaos-powered Knuckles and Dr. Finitevus.
Equestria in The Son Of The Emperor uses a magical barrier to isolate itself from the rest of the world. No one on the outside knows anything about it.
Star Wars, Episode 1, has the Gungan city, which meets all the requirements easily. Hidden apart from the rest of the world (underwater), main character (Jar-Jar) comes from there, and later they return to get the gungans to fight alongside them in the final battle.
Gondolin, Doriath, Nargothrond, Rivendell, and Lothlórien are all examples, if this trope allows for very large populations, advanced technology (for the setting), expeditionary armies, and large political ambitions. That said, some of them (especially Gondolin, Doriath, and Nargothrond) do have periods of isolation along this trope's lines, and two of them (Gondolin and Nargothrond) meet horrible ends at the hands of the Big Bad they were hiding from.
The Shire, however, is a classic Hidden Elf Village, apart from the dumpiness and furriness (and non-Elvishness) of its inhabitants (and the fact that there was no actual policy behind it — the inhabitants were just homebodies that were missed by the general collapse of civilization in the area rather than people that actually went out of their way to hide).
The various forms of Tanelorn in Michael Moorcock's writings, a city which exists as a sort of cosmic rest stop for the Eternal Champion, who nonetheless is always compelled to leave eventually.
Gormenghast might qualify, although to what extent its isolation is intentional isn't clear.
Literary example: In the Dragon Wars Saga, the elf realms of Andur'Blough Inninness and Tymwyvenne are both extremely secretive and magically protected (the former by a spell which prevents explorers from finding the place without being guided there, the latter by zombies and sleep-inducing pollen).
Kevin J. Anderson's Gamearth Trilogy has a female player sneak into the game room at night paint a Hidden Elf Village on a single tile of the hexagonal world map, then paint over it. Since the game is magic and their PCs are rapidly becoming self-aware, when the party lands on the seemingly blank space the next morning, the village is there, waiting for them.
In Tad Williams' Memory, Sorrow, and Thorn series, the Sithi city of Jao é-tinukai'i is one of these. To be fair, they had plenty of justification: they were on the losing end of a catastrophic war and had been hunted by humans for centuries thereafter. That doesn't stop their Always Chaotic Evil counterparts, the Norns, from taking advantage of their isolationism to wreak all kinds of havoc, up to and including unleashing an unstoppable undeadhorror on the land. Furthermore, both the Sithi and Norns are exiles from a mythical land far to the west of Osten Ard known as the Garden.
The entire Land of Oz, situated as it is inside an impenetrable desert that kills anyone who tries to cross it.
In Lilith's Brood by Octavia Butler, there is a hidden mountain village where the citizens have become so isolated from the rest of the world that they all suffer horrible genetic diseases from inbreeding.
The entire Wizarding World in Harry Potter, to the point where some members are completely incapable of functioning outside their little enclaves. Of course some of these don't function too well even inside their own little world.
lampshaded in Terry Brook's Shannara collection, where it's pointed out in Elfstones that while the Elves and other Faerie creatures used to live by this standard, it aided in general apocalypse and thus when humanity started to rebuild, they joined the newly formed races.
Becomes a plot point in the later Scions of Shannara series, where due to the arrival of the Shadowen, the Elves have once again formed a Hidden Elf Village, and it's absolutely necessary to bring them back.
The Wheel of Time has several, most notably the Sea Folk isle of Tremalking and its surrounding archipelago, the Aiel holds (though those are more of "we kill you (or let you die of thirst) if you set foot on our land without things to sell us and we come out and kill you if you do something really, really dumb like chopping down that wonderous tree we gave you generations ago"), and the land of Shara.
You could technically count the Two Rivers, too, since until the middle of the series they were so isolated they were still using thatch roof and had next to no affiliation to the country they're part of.
And more than any of the above, the Steddings.
Even has a weird Evil Counterpart in the town known only as "The Town," in the valley of Thakan'dar near Shayol Ghul, whose inhabitants serve the Big Bad.
In The Dark Tower: The Waste Lands by Stephen King, Eddie hopes to find this in the devastated city of Lud. Even saying, "Bring on those wise f*** in' Elves."
At the time, Eddie had just left the closest thing he was likely to find to a Hidden Elf Village in the Crapsack World of the Dark Tower, a hidden village of elderly folks who are always hiding from bandits and disguise their town as abandoned ruins by, well, living in a ruined town and not going outside a lot. They don't offer much in the way of sagely advice or magical / technological help, but they do set a mean table.
The Tswana, as introduced in Empire of Ivory, is best described as a Hidden Dragon Empire... that forgoes the 'Hidden' part when they "abolish" the European slave ports.
In the Sime Gen series the Rathorites are a secret society/hidden community who have tools that could go a long way towards fixing the problems of the world, but won't reveal them because they could be misused.
Time Scout: Time Terminal 86 is hidden in a warren of tunnels inside the mountains of Himalaya.
Percy Jackson and the Olympians: Camp Half-Blood may count as it also posseses magic barriers aside from just hiding the demigods, but the sequel series Heroes of Olympus has Camp Jupiter and adjoining city of New Rome.
In the Web Serial NovelTheatrica, the city of the same name transpires to be perfectly hidden from the outside world, as its people, the Theatricans, are xenophobes.
For years Xanth was one, ever since King Roogna set up a magic shield that killed anything crossing between Xanth and Mundania (our world). The only people allowed through were those being exiled. This ends when "Evil Magician" Trent manages to get back in, and discovers to his horror that the centuries of isolation have led to magical inbreeding, which will in time lead to the extinction of humans in Xanth. When he takes over, he takes down the shield and encourages his own followers to marry locals to keep the gene pool clean.
The Oompa-Loompas of Charlie and the Chocolate Factory come from Loompaland, a Death World of fearsome predators. The little people created a Tree Top Town to afford some safety, but it wasn't an ideal situation because there was virtually nothing decent for them to eat. When Willy Wonka, in need of a new workforce at the time, discovered them and learned that more than anything else, they craved cacao beans (the basis of chocolate), he made them an offer: If they'd come and work for him, they could live in his factory — an Elaborate Underground Base — and have all the cacao beans they wished. They jumped at the offer, and he secretly transported the entire tribe to his factory. Moving from one form of isolation to another (owing to Mr. Wonka's determination to keep spies out of the factory, the reason he sacked his original workforce), they were able to create a new system of villages and towns in the factory.
And over on Stargate Atlantis, the Asgard discovered in the Pegasus Galaxy had hidden themselves away on a toxic planet through and since the Wraith/Ancient war.
Andromeda had Terazed, a planet in an out-of-the-way slipstream colonized by human and Nietzschean Commonwealth loyalists led by Dylan Hunt's former fiance. Thanks to a bit of time travel they knew that in 300 years Dylan and the Andromeda Ascendant would escape the black hole and attempt to rebuild the Commonwealth, so they prepared to reveal themselves at that time and became the restored Commonwealth's capital.
Also, Tarn-Vedra, the capital of the old Commonwealth, cut itself off from the slipstream through tesseract at the start of the Long Night. Eventually the Vedrans themselves evolved into seemingly omnipresent beings and the "Seefra" system accumulated refugees from all over space, the final season largely takes place there.
Robert Hewitt Wolfe (original, and fired, developer of the series) revealed after the show had concluded that if he had been allowed to pursue his original plan, Tarn-Vedra would have been dragged into the Magog conflict by force. He also responded to a question at the Ex Isle forums about whether the Vedrans had removed themselves from the connected universe out of selfishness or a desire to build up for the invasion with "They probably told themselves the latter while secretly knowing that it was the former.", making them actually fit the trope a bit better on both ends.
Wonder Woman TV Series: Paradise Island is an uncharted island within the devil’s triangle. Queen Hippolyta has decided to occult Paradise Island from the world: In the pilot, she claims that no one in the last thousand years has ever found it. She also claims that any amazon who left the island may lost her immortality and become a mortal again.
The Druids from Merlin have these settlements in the forests around Camelot, hiding from the laws that would have them killed for their innate magical powers.
Thunder Mountain in Jeremiah is a Cold War bunker housing the now grown up children of the military and government officials, who spent the entire virus outbreak and subsequent chaos keeping the old world and civilization intact. After the pilot episode, they decide to secretly work to rebuild the world, and cause a renaissance.
On the flipside, there is Valhalla Sector, which is the government and military leaders that were responsible for the virus base where they planned to restart the American government through force.
As RPG settings have grown in size and scope, so too have their Hidden Elf Villages. For example, both the Shadowrun and Iron Kingdoms campaign settings have Hidden Elf Nations: Tir Tairngire and Tir na nOg in Shadowrun, and Ios in the IK. D&D'sEberron campaign setting takes this a step further with Aerenal, a whole Hidden Elf Continent.
Aerenal is small though. Argonnessen is a Hidden Dragon Continent!
Although they aren't so much "hidden" as they are "we're right here, but we'll kill you if you set foot here without the correct forms, filled in in triplicate."
As Shadowrun is set in Earth 2050+ AD, Tir Tairngire and Tir na nOg occupy Oregon and Ireland, respectively. A lot of people are very annoyed.
The World of Greyhawk has a Hidden Elf Nation in the country of Celene, which refused to help its neighbours in the wars against the evil creatures that invaded them. Naturally, this generated a lot of ill will towards Celene. The elven race as a whole, though, is more nuanced in that they don't actually have anything against most other races and will provide help to refugees seeking food and heroes seeking aid, but are simply more comfortable living in their own communities than they are living among humans or other races. Even within Celene itself, there's a sizable number of elves who disagree with their queen's decision to stay out of the surrounding conflicts and actively work to help their human and dwarven neighbours.
Even among the Craftworld Eldar, the ones from Craftworld Dorhai have this trope as their hat. Bizarrely, they believe that all Eldar not from Dorhai are "tainted", and refuse all dealings with them. The other Eldar are puzzled by this, to say the least.
Warhammer Wood Elves, of which Exodites are the futuristic expy also qualify for this trope. And being Warhammer, they are of the highly xenophobic, and will kill you if you set foot in their forest unwelcomed. That is if the forest they live in doesn't kill you first.
Warhammer Fantasy's High Elves are also highly isolationist and bar non-Elves from their nation of Ulthuan (though they tolerate non-Elf visitors in the gateway city of Lothern).
And the Dark Elf lands are not open to visitors. At all. Any attempt to enter peacefully will probably result in slavery (well, you get in technically) or a barrage of massively poisoned crossbow quarrels.
The Chaos Dwarfs reside in Zharr-Naggrund a massive ziggurat city in the Mountains of Mourn. There not many visitors there save for the Chaos warbands who trade thousands of slaves for the Chaos Dwarfs war machines.
Numenera has the Weal of Baz, a village inhabited exclusively by sapient machines. It's heavily guarded and camouflaged with hologram emitters, since the humans of the Ninth World tend to think of all automatons as property.
Within Dragon Quest III, the elven queen put a sleeping curse on a nearby town because her daughter went on an Interspecies Romance, which was forbidden. But even after realizing that her daughter left willfully, she still doesn't like humans.
Final Fantasy VIII also has the nation of Esthar, which spent seventeen years as a Hidden Elf Country.
Garifs of FFXII are a much more lighthearted version of this trope, though unlike Vieras: Garif laws aren't as strict, leaving the village is allowed, they have less of a distaste for outsiders(though they do show concern for how humes are violating the world), and Garif do eventually begin to consider getting involved with the outside world. The Garif are all Proud Warrior Race Guys and will practically give non-Garif proud warriors full access to the village(as is the situation with the game's main characters).
The Final Fantasy IX example however is more justified then the others: Black Mages are basically Golems and gain sentience somewhere along the way, the village being a hideout for them to escape the Big Bad who created them. It doesn't work. Vivi is a special case and is vaguely hinted to be the prototype.
So is the whirlwind shrouded Cleyra, an off-shoot of another town.
Going back to Final Fantasy III, there's also the Dark Knight village, and Doga's Village, although they, and Tozus, aren't really of the xenophobic variety. They are actually a really good way to get powerful weapons and spells.
Tales of Symphonia has Heimdall, where many of the main characters (including the Big Bad) come from. Entering this village requires a writ of passage from the King of Tethe'alla, and even with it in hand, guards at the front of the village ban the half-elf members of your party from entering the village. For some reason, half-elves are pretty plentiful in both worlds (much more so than actual elves), despite there being only one village of elves that never associates with humans.
Talking to the residents of Exire, the hidden half-elf village confirms that the children of two half-elves are also half-elves.
A successful example. Its so well hidden its unaffected by the turmoil on the ground.
Somehow, four thousand years later, in Tales of Phantasia, its even better hidden, and now has another hidden village (specifically, a Ninja village) inside of it, like an isolationist Russian doll.
Tales of Symphonia also has Mizuho, a Hidden Ninja Village. Though in contrast to most examples, Mizuho is known for taking an interest in the outside world thanks to its intelligence network, those the village itself is still highly isolationist. At least until the hero's party arrives and makes an alliance with them, thanks to party member and Mizuho citizen Sheena and Reasonable Authority Figure Tiga.
The original Vault 13 in Fallout 1 was a clear-cut Hidden Elf Village, only getting in touch with the "savage" outside world when their own continued existence depended on it.
This is a running theme in Fallout 2, with Vault City, San Francisco and the Enclave, each more secluded and hostile to outsiders than the last.
By the time of the game Vault 13 has become a home for friendly, intelligent deathclaws, and a few humans who have settled in with them.
This is a running theme in the Fallout series generally, since Vault 101 in Fallout 3 also avoids any contact at all with the outside.
Which becomes quite a problem about halfway through the game.
Most of the examples are Vaults or the descendant polities of Vaults, which makes sense - the public purpose of the Vaults were to allow people that entered them to survive the atomic apocalypse, to re-emerge when the worst was over. The Vaults that actually did have that purpose tended to emerge into a world where the most common visitors were roving bands of bandits or monstrous beings (and where they were the only ones around to have kept a measure of high technology and an historical record). Add to that Vaults whose actual purpose required/was long-term isolation, like Vault 13 and Vault 101...
Fallout: New Vegas has Nellis Air Force Base, populated by the Boomers, a highly isolationist faction obsessed with firepower and all too willing to use it upon outsiders who get too close to them. There's also Jacobstown, a small ski resort populated by mostly peaceful Super Mutants that isn't exactly a secret (though it is fairly remote) is generally left alone by the populace, and Hidden Valley Bunker, home to a remnant of the also isolationist Brotherhood of Steel.
Fallout is full of cloistered communities, more or less isolated by distance and lack of infrastructure, and naturally wary of outsiders. Little Lamplight is one of the most hidden, and Bigtown by contrast suffers for its openness.
In Wild ARMs, the elf-like race of Elws transported their land to another dimension so that they won't have to experience the decay of the world resulting from the previous war.
Suikoden III has a rare example of a non-elf Hidden Elf Village in an elf-bearing setting. The "Grasslanders" of Alma Kinan live in a deep forest behind an illusory veil or barrier of some sort, only emerging at the behest of their seers. They have a much more "elfin" style than the elves of the setting, who are more like Tolkien's Noldor.
The elves of Na-Nal from Suikoden IV hide in the forest as well, and consider themselves superior to the human natives. In reality, though, they're Not So Different: both sides are equally arrogant, and this leads to disaster. Ironically, in this instance the hidden village works, allowing the elves to pull a Karma Houdini after provoking a massacre.
Alseid from Suikoden V fits this trope exactly, with the elves vowing to stay separate from the "barbarous humans". Pretty much every non-human race is like this to begin with, as part of a "Accept People For Who They Are/Racism Is Bad" Stock Aesop.
Suikoden V's Beavers also mostly keep to themselves, not wanting to get too involved in the "humans' war". However, they haven't actually hidden their village, which has the expected results when the Godwins decide to go skipping across the Moral Event Horizon and indulge in a little genocide. This naturally leads to your rebellion pulling a Big Damn Heroes and the beavers deciding to be Neutral No Longer.
This goes all the way back to the first game, where the elves aren't just isolationist, but so racist that they are disgusted when Kirkis leaves the village to seek help from the human Liberation Army on hearing of Imperial plans to destroy them. Of course he's right. The village ends up torched to the ground by Kwanda's Burning Mirror.
Every Fire Emblem game has a Hidden Dragon Village where the humanoid Manakete dragons live. The exception being Fire Emblem: Path of Radiance and Radiant Dawn, those games have a Hidden Branded Village. Branded are exiled from society for being half-Beorc (human) and half-Laguz (a humanoid race who can turn into animals). The Dragon Laguz have a not-so-hidden country where they don't let anyone else in.
An example that doesn't apply for dragons is the Spirit Village in the kingdom of Verdane in Geneaology of the Holy War, and it also hides a nasty secret - the descendants of the dark god Loptyr, or more specifically, the priest Maira, the original man who held minor Loptyr blood, all live there to protect themselves from the outside world. Deidre, Sigurd's wife, originally lived here, as did her mother.
A plot-important village is the Elibe games' village of Arcadia, located in an obscure part of the Nabata Desert. It's a village where humans and dragons live in harmony, much like they did before the Scouring.
Shining Force II had the hidden fairy village, but it was more of a bonus area than anything. Pretty much the only notable things about it are a promotion item you can find in a chest and a bonus fight against infinitely spawning monsters (very useful for powerleveling, but it can be beaten by blocking the spawn points).
There is also a second hidden elf village near the end of the game that lets you talk to The Blacksmith who can craft the best items in the game for each class, finally making a use for all the Mithril you have collected.
To be fair, Kokiri are not elves...but they are rather elf-like.
The Kokiri have the excuse that if they leave the forest, they die, which makes their isolationism very understandable. They also have no problem whatsoever with visitors - so it's more a case of circumstance than policy.
Zelda II: The Adventure of Link also had an example of this, with a town in the later part of the game that required you to remove the right patch of trees in a forest to reveal it.
Romancing SaGa has Merholm, a small village hidden beneath some ruins deep in the desert. In this case, though, it's already been used once, the last time the gods broke the world. The survivors emerged to discover that humanity had been remade without them, and became the Taralian tribe... and generations later, when it looked like the war between the gods was heating up again, their descendants headed back to Merholm to wait it out.
Secret of Mana has a village of, well not Elves, but Moogles. And you had to walk around a multiseasonal four screen forest until you unlock it.
Played much straighter in the sequel, Seiken Densetsu 3, where the Elf Village Diorre is hidden deep within the Lampflower Forest. To find it, players have to search at night, when the eponymous flowers glow, and those that lead towards the village have a different color from the others. Naturally, the elves are isolationist and unfriendly, and even when they recognize that you're trying to save the world, still charge for items and lodging. And to complete the trope, the party member Carlie is the village's bastard princess on her mother's side.
The Guild of Weavers in Loom isolated themselves on an island community after being accused of witchcraft and chose to ignore the rest of the world.
BioShock Infinite has an aversion. The flying city of Columbia was built as a demonstration of American ingenuity, so the designers wanted to show it off, and everyone knows about it. Which is then subverted in that the mysterious strangers actions seem to imply that getting there is a pain. It makes sense, since not only does the game takes place before the proliferation of airplanes and the invention of radar, but while everyone knows that Columbia exists, no one knows where it went. It's then played straight later, because nobody knows about it even in The Eighties, when those things are commonplace.
RuneScape has Lletya, where - well, there aren't many points of interest here...
The entire country of Tiranwyn could count as hidden, since there is almost no contact with other countries. The main city is ruled by the Iorworth clan, who are the villains of the elf quest series. Lletya is the base of the rebel elves, and you report there during the elf quests frequently.
The High Elves also have out-of-the-way holdouts in Plaguelands and Hinterlands.
Not so much in the Plaguelands anymore., as they've all been, um, transformed as of Cataclysm.
All elf societies work on this to some degree. Before the wars and to varying degrees after, the Night Elves were almost completely reclusive. The Blood Elves also seem to be interested in just keeping to themselves for the most part.
Pandaria has remain hidden from the rest of the World for thousands of years, due to a magical mist that hides it from the rest of Azeroth. It was until a clash from the Alliance and Horde fleets who stumble upon it by chance.
The Dragon Age, the Dalish tribes are nomadic and frequently move their hidden elf villages around. This is due to their mistrust of the humans who in the past destroyed two of their homelands. The Tevinters enslaved them for a thousand years and caused them to lose their immortality, while the Andrastian Chantry lead a Holy War against their former allies and stripped the Canticle of Shartan, the writings and tale of the Dalish general who lead Andraste's army, completely from the Chant of Light.
During the First Blight, as the Darkspawn swarmed the Deep Roads that connected the Dwarven Empire, the old Thaigs and Cities fell one by one, eventually forcing the Dwarves to retreat to Orzammar and seal the gates behind them, effectively cutting themselves off to weather the storm. A thousand years later, the city of Kal-Sharok was discovered to have also miraculously survived the onslaught, but the inhabitants are said to have never forgiven Orzammar for leaving them to their fate.
Mass Effect 2 reveals that the Always Chaotic EvilKiller Robot geth are in fact the terrorist outcasts of a Hidden Elf Civilization, thus demonstrating yet another problem with the trope; if most of you just sit in your peaceful utopia, all most will see of you are the vicious jerks who go out and raise hell. Galactic Interpretation: All Geth Are Killer Robots.
The batarians have a similar problem; their withdrawl from the Citadel (hub of interstellar diplomacy and trade) means that only the pirates still interact with the galaxy. Galactic Interpretation: All Batarians Are Pirates.
The Quarians, having been forced to become a civilization of nomads, simply lack the resources to maintain prisons or the numbers to afford executions, meaning they exile everyone they don't fine, though children of exiles are innocent of their parent's crimes and are freely welcomed back to the flotilla. Unfortunately this means the only members of the species most encounter (other than the occasional Naïve Newcomer on Pilgrimage) are the jerks the other Quarians couldn't stand, i.e. con artists to serial killers. Galactic Interpretation: All Quarians Are Crooks.
In the Mass Effect 3 DLC Leviathan the race of Leviathan that actually indirectly built the reapers hid under water for literally billions of years to not get involved in the eternal galactic struggle.
Crystalis has the village of Oak, which is more of a Hidden Dwarf Village.
Odin Sphere has Pooka Village, where those who received the Pooka curse gather and try to collect all the Valentine coins.
In Golden Sun, Vale is this, keeping themselves secret so knowledge of Psynergy doesn't get out. Shaman Village fits, too —when you arrive, the inhabitants won't even speak to you. Garoh is a hidden werewolf village, whose inhabitants (rightfully) fear the Fantastic Racism of humans. Lemuria also fits the description nicely, to the point of banishing a citizen who'd dared help our heroes and join them on their quest.
Ayuthay initially appears to be this in Dark Dawn, but it's justified: they're under a siege at the time.
Dark Cloud features Brownboo village where the moon people live. They're out of sight and danger which is how they prefer it.
Kingdom of Loathing has one when ascended under a Mysticality sign. What, you say you're Canadian yourself and not elfin in the slightest? Well, they are at least portrayed as studious, reclusive, living with nature and somewhat well-adorned, quite within the common fold of elven tropes.
In Touhou, the Lunar Capital was founded by people who fled the Earth in ancient times to escape its "impurity" (aka life and death), and is kept hidden by a barrier. Mortal beings who manage to reach the Capital (usually by accident) are turned away to prevent them from contaminating it.
Gensokyo itself was created to preserve magical beings from a world that was disbelievingmagic.
Skies of Arcadia has the Silver Moon settlement, birthplace of main character Fina, which appears to fit this trope, having removed itself from the world during the ancient war and thus survived the devastating cataclysm that affected all the other ancient civilizations. Ultimately subverted when the Dark Secret of their immortal Elders is revealed: they caused the ancient cataclysm intentionally, after leaving the surface of the planet, in order to wipe out the enemies they left behind (i.e. everyone else on the planet). They aren't so much a hidden village as they are a bunker of genocidal Knight Templars, waiting to see if they should use their doomsday device again to finish off the descendants of any survivors who might threaten them
Two other examples would be Yafutoma, to a degree, as it is blocked off by the Dark Rift, and Glacia, the doomed capital of the old Purple Civilization - it was built under a landmass, so it survived the Rains of Destruction, but unlike other examples, all of its people have disappeared.
Oasis in Fallout 3, a nature cult in a hidden valley who worship the FEV experiment Harold, who has gradually transformed into a sentient tree. The whole valley is a New Eden of lush vegetation which is only a rumour in the wider wasteland.
Arboria from WildStar was this trope on the scale of an entire planet, until the Exiles stumbled upon it. Unfortunately, so did the Dominion, and now there's not much of a "Village" to speak of, either.
You can find settlements of elves surrounded by mountains in One Way Heroics, who claim they are not interested in your quest to stop the advance of the darkness, even though by the time you find them they are hours away from being destroyed by it.
In Drowtales, drow, the underworld dwelling ancestors of Dark and Light elf refugees who fled to the underground to escape a devastating war believed all Light and Dark elf cities had been completely destroyed and the only elves that reminded existed in scattered settlements or as slave in their cities. It is eventually discovered at least one such city still exists, in near absolute isolation from the outside world and under an extremely oppressive and corrupt regime, that kills anyone who finds their city in secret.
The Hidden Elf Village in RPG World. This is eventually worked into the plot (if you can say RPG World has a plot); once, every N years, a competition of sorts happens between the Elves, Humans and Monsters to decide the dominant race on the planet. Since humans won the last one, Elves are forced to stay (en masse) in their village and can't settle elsewhere; they can leave their village, but are nomads if they do. Similarly, monsters are forced to stay in South City, or lose their minds and become the wandering monsters that the RPG Elementswebcomic relies on.
The Seven Villages of the Racconnans in Tales of the Questor are hidden behind an artificial swamp and an enchanted fog. The reason being that they were persecuted by the other species for their magic-like lux abilities. Though that decision is starting to bite them in the ass centuries down the line because they're running out of resources, two political parties have formed to figure out whether they should expand the Mistwall or attempt trading with outsiders.
In The Gamers Alliance, the biggest elven cities Sanae, Tel'Elee and Illunii are all hidden in forests.
Avatar: The Last Airbender: Ba Sing Se under Long Feng blatantly ignores the ongoing war. Brainwashing ensues. The Northern Water Tribe (which also avoided the war for ages) and to a lesser extent the Air Temples are similarly isolated, due to practicality and location.
The Smurfs! At least in the original books and the first few seasons of the TV show. In The Smurfs and the Magic Flute, the Smurf Village could be reached by humans only through a magical method called "hypnokinesis".
Paradron of The Transformers and The New Crystal City of The Transformers IDW are both isolated, pacifist colonies of neutral Transformers who have managed to avoid being drawn into the eons long Great War.
Amish, Old Order Mennonites, most orders of monks (Christian or Buddhist) and other "non-wandering" ascetic or mystic sects usually abide by the "non-subverted" version of this trope. The Amish in particular pledge to "live in this world but not of it." They do let their kids live in the outside world for a time before deciding to stay in the order.
Subverted in the case of the original Buddhist kingdom in Tibet commonly identified as Shangri-La. It was indeed a peaceful and enlightened place that welcomed and made peace with visiting Jesuit missionaries in the 1600s... until the kingdom was invaded and burned to the ground by a rival Buddhist Tibetan group that was angry at them for tolerating Christians.
The Fundamentalist Latter-Day Saints compounds.
The policy of Isolationism is similar to this on a national scale.
North Korea's isolation qualifies it as a Hidden Elf Country. Or a "Hidden Something Country"—North Korea is famously not a nice place to live, unless you're a Party member.
Japan under the Tokugawa Shogunate was within spitting distance of this trope.
And thus the trope swallows its own tail as the elf village trope, so common in Japanese videogames, is likely inspired loosely by history.
For much of the nineteenth century, the United States practiced a policy of non-interventionism, which turned into full-on isolationism in the period between the two World Wars.
Korea, once called the Hermit Kingdom.
Both Japan and Korea's internets by means of language barrier. The latter going as far as to save all its text as images, and if that's not possible, routinely block web translation sites like Google.
And the rabbit hole goes deeper to a somehow more literal level. Japan's national internets containing a bundle of core websites locked out unless you have access to an active Japanese mobile phone or .edu university or fauxiversity webmail, and Korea's quite literally requiring a national ID AND a specific digit on the ID identifiying you of not just Korean residence but also Korean RACE. Extending to much of the nation's private websites on account of them being published via a corporate web-hub duopoly subscribing to the authentication ideals. Geeeeeeez.
While it's started to open up somewhat in recent years, Bhutan still counts even today. Unlike other such modern-day countries, it actually maintains its status of a Kingdom!
The Hawaiian island Ni'ihau, also known as "The Forbidden Isle".
There are several tribes in the Amazon Basin who have chosen to disappear, retreating into the rain forest's deep interior rather than maintain contact with the rest of the world. They know all about modern civilization, and want nothing to do with it.
The Maya city of Tayasal, situated on an island in Lake Peten Itza deep in the Guatemalan jungle, was known by the Spaniards since Cortés himself scouted the region in 1525, but remained unconquered and unchristianized until 1697, a wooping 170 years later. It wasn't exactly a village either: records of the time note that it had 21 functioning temples, as much as the famous archaeological site of Chichen Itza.