As bad as Heavenside from Doktor Sleepless is, most people consider it an ironic name, but it was actually a contrast to Hellside the even worse city on the other side of the mountain where "everyone died."
In Batman Begins, there's the League of Shadows which is an ancient secret organization that takes upon itself to destroy societies and cities that, according to their standards, have become too corrupt and decadent. ("The League of Shadows has been a check against human corruption for thousands of years. We sacked Rome. Loaded trade ships with plague rats. Burned London to the ground. Every time a civilization reaches the pinnacle of its decadence, we return to restore the balance.") Next on their list: Gotham City. And then they show up again years later, trying to do the same thing, under the command of Ra's al-Ghul's daughter in The Dark Knight Rises.
Coruscant in the Star Wars prequels shows signs of this, as does the Old Republic generally. At least, according to the Empire's propaganda. To be fair, the fact that they could and circumstances surrounding their willingly voting in the empire and its new and oppressive system does, ironically, illustrate it nicely.
Texas City, CA in Breaker Breaker. An abandoned mining town re-incorporated by what the film, at first, seemed to hint was a band of traveling gypsies (but later just turned them in to 70's-style corrupt hicks), and funded by bootlegging and hijacking 18-wheelers. Gets destroyed in the end by a band of vengeful truckers responding to a distress call on behalf of the film's hero, JD.
Númenor in J. R. R. Tolkien's The Silmarillion. After Sauron is taken captive by the Númenóreans, he converts them to Melkor worship and tricks them into sailing to Valinor and violating the Ban on setting foot there. As a result, the Valar call upon Eru Ilúvatar and he destroys Númenor with a giant wave, sinking it beneath the sea.
Andre Norton's "Operation Time Search". In our real world, Atlantis fell under the control of evil rulers and was destroyed. The actions of the hero prevent this, and as a result history is changed and Atlantis survives to the present day.
The city of Brussels, Belgium, appears this way in retrospect to Marlow in Heart of Darkness.
The Emerald City has shades of this even in The Wizard of Oz. It's downplayed, sure, because Dorothy doesn't perceive any real unhappiness or corruption in its people, but the ruler is a two-bit humbug phony playing the whole city for fools. And the lovely "emerald" color of the city? Just colored glasses that everyone is required, by law, to wear.
Like everything else in Oz, the depiction is even worse in Wicked. Booze-soaked nightclubs, whores on every corner, chamberpot contents in the street, the Unionist church's KnightTemplars running unchecked, and a brute posing as a wizard cheerfully exploiting all of it to keep in power.
The Thran Empire, particularly the city of Halcyon, that served as Precursors to the main setting for Magic: The Gathering is shown to be one of these in its titular novel, The Thran. Even before Yawgmoth started pulling their strings, they practiced Fantastic Racism against the goblins and other species, were much more concerned with aesthetic beauty than people's safety or comfort, created a massive undercity of caves where all the undesirables (both criminals and people who merely disagreed with the way of doing things) and had a superstitious understanding of disease (which they believed was caused by evil spirits....granted that was sometimes true in Dominaria, just not most of the time. After Yawgmoth...
Charn from The Magician's Nephew, the prequel to The Chronicles of Narnia. The civilization (and the entire universe in which it existed) was destroyed by the Empress Jadis, who killed every single living organism just because she couldn't be queen. She kept herself preserved as Sealed Evil in a Can until two kids from another universe freed her from her slumber (they had been tempted by the Schmuck Bait-laden mechanism used to awaken her). Then she hitched a ride with the kids back to their universe, and eventually to Narnia, where she became known as the White Witch.
The city of Shadukiam in The Orphan's Tales. In "The Book of the Sea" we learn about how its rich inhabitants care about nothing but aesthetics and money, devouring ridiculous delicacies made of jewels and forcing their species minorities to live in ghettos. In "The Book of the Storm," we learn of how the city met its terrible end, lost its anchoring in the world, and became the hollow nightmare city of Marrow.
New Babylon, by virtue of destiny, becomes this in the Left Behind books.
Magrast in The Chronicles of Magravandias. The city is pretty much the concentrated corruption of the entire Magravandian empire, and the palace in particularly bad.
Religion And Mythology
In The Bible, there's, of course, Sodom and Gomorrah. The destruction of these cities is the subject of the 1852 painting by John Martin that's the image for this page.
The medieval city of Vineta was, according to legend, a rich and powerful port on the Baltic Sea located near the present-day border of Germany and Poland. The sinfulness of its inhabitants led God to destroy it with thunderbolts and sink it underneath a storm tide.
In The Book of Mormon, the city Ammonihah is destroyed by an army of the Lamanites after they rejected the words of the prophet and killed those that did believe. They were pretty sure God couldn't destroy their great city in a day as prophecied if they didn't repent.
More broadly, the Nephite and Jaredite nations near the end of them. They did pretty deplorable things at the end.
In Phantasy Star II, the entire human civilization of the Algo system is dependent on Mother Brain. This leads to complacency, and the world is unable to handle it when she starts going bonkers on them.
Varric: Kirkwall, "The City of Chains". Long ago it was part of the Imperium, slaves coming from far and wide to work the quarries. Now it's a Free City... but I use the word loosely
Pathologic features a Soiled City in a Steppe. Depending on the ending you end up with, this trope is more or less relevant.
In Hector: Badge of Carnage, the villain's plan is to use a Hate Plague on the residents of Clapper's Wreake so that they kill each other, wiping the slate clean and allowing him to create a better city.
Rapture in BioShock the city has been torn apart by a war between Ryan and Atlas, and only ones left are insane splicers who are only interested in finding more ADAM for them to harvest.
Columbia from Bioshock Infinite. Sure it's a beautiful city. Sure it has beautiful parks, gorgeous architecture, and the honour system in use at shops. But there's a price to that pretty. And it is ugly.
Fallout 3: In the decades preceding the game, the Pitt, formerly the industrial giant Pittsburgh, was a lawless Polluted Wasteland inhabited by rape gangs, raiders, slavers, and various horrific mutants. Upon discovering the city, Lyons' chapter of the Brotherhood of Steel initiated the Scourge, which wiped out most of the population except for a few unmutated children who were placed into initiate training, one of which was Paladin Kodiak. After being left for dead in an explosion and rescued by scavengers, Paladin Ashur became the leader of the city.
Nipton from Fallout: New Vegas was populated by gamblers, thieves and prostitutes, until the Legion laid waste to the town and executed or enslaved the residents.
Ba Sing Se, capital of the Earth Kingdom, was once the greatest city in the Avatar: The Last Airbender world. But over time, thanks to Evil Chancellor Long Feng and his Secret Police, it has degenerated into an Orwellian dystopia where brainwashing abounds, poor people are kept in segregated neighborhoods, and people are forbidden to even mention the war that's been raging outside the city for a hundred years. And just when Long Feng was arrested and things were starting to look up, Princess Azula of the Fire Nation infiltrated Ba Sing Se, got the Secret Police on her side, and finally captured the city and the entire Earth Kingdom.
The Legend of Korra: Republic City is worse, the city is filled with mafia benders, and ran by bureaucrats who aren't doing much with the unequal treatment of non-benders. Finally things erupted to war, when the Equalist terrorist took over the city in a full scale attack.
On the Arabian Peninsula, there was Iram of the Pillars—the "Atlantis of the Sands". In Islamic legend, Iram of the Pillars (also known as Ubar) was a city of untold riches that was buried under the desert sands as punishment for defying God. Long thought to be a myth, satellite photos and recent archeological excavations have indicated such a city probably existed until around 300 AD—about 300 years before the birth of The Prophet Muhammad, i.e. long enough for it to become the stuff of legend.
Rungholt was a thriving German merchant city on the North Sea coast until it was destroyed by a storm tide in 1362. Legend attributed its destruction to the rampant greed of its citizens and acts of sacrilege against God.
The low-lying Dutch city of Saeftinghe was a prosperous trading center from the 14th to the 16th century until much of the land surrounding it was lost to a disasterous flood in 1570. The city itself was abandoned in 1584 when, during the Dutch War for Independence, Dutch soldiers were forced to destroy the dike that protected Saeftinghe resulting in its sinking into the marshy bogs of the Schelde River. In Dutch folklore, Saeftinghe was an ornately rich but avaricious city that ultimately paid for its Greed by sinking into the salty marshlands after being cursed by a merman for refusing to set his captured mermaid wife free.
Port Royal was an open haven for pirates and smugglers during the 17th century with economy largely based around boozing, whoring, and stealing. Like Sodom and Gomorrah, it was destroyed by an earthquake in 1692 that caused it to sink into the sea.
Tsarist Russia as a whole. What accelerated its fall was the too much income inequality and injustice. The New Russia in the nineties was approaching the late-Imperial level of decadence and injustice amazingly fast.
The incredibly deadly and destructive Lisbon Earthquake of 1755 represents a real-life inversion of this trope. After the quake shook the city for five minutes, most of the population took refuge on the waterfront where, 40 minutes later, a tsunami hit. In the aftermath, virtually everything that hadn't collapsed or gotten flooded was destroyed by fire. Because the city wasn't much of a Wretched Hive and the quake struck on All Saints' Day, it lead to a lot of philosophical exploration of theodicy, i.e., why do bad things happen in a world governed by a good deity? Most of the Enlightenment's great thinkers were influenced by the Lisbon Earthquake, with Kant and Voltaire writing works that discussed it directly.
Saint-Pierre, Martinique, the "Paris of the Caribbean", was destroyed twice, first by a hurricane in 1780, then more completely by a volcanic eruption in 1902.