Under City

This used to be part of a sprawling metropolis, or maybe it was a whole city of its own, but something happened. Maybe an earthquake buried it, or maybe they just decided to build new city on top of it and in time forgot the old one.

This isn't just any underground area; the Under City used to be above the earth before being buried by whatever occurrence. Could be a whole Ghost City, or a part of Absurdly Spacious Sewer.

Anime and Manga

 * In the first anime of Fullmetal Alchemist, there is a hidden city
 * Berserk has a massive prison tower built on the ruins of an older city.

Comic Books

 * Underground Duckburg in Don Rosa's version of Donald Duck universe.
 * When the old Spider Man villain, Venom, had his own comic released, he spent the first storyarc in a section of San Francisco that was buried and contained 1800's-era architecture (the city had simply built over it for some reason). Sadly, this was all mostly forgotten by the next miniseries.

Film

 * Star Wars has Coruscant, where the ground is always buried under at least five layers of ancient skyscrapers.

Literature

 * The Undertown in The Dresden Files is located under Chicago, consisting of old buildings that sank into the ground under their own weight. It is populated by various supernatural nasties.
 * Neil Gaiman's Neverwhere has a London Below which consists largely of places buried and forgotten by London Above.
 * Ankh-Morpork in Discworld novels: Because the city is built on soft loam, near an extremely turgid river, the ground levels of its buildings find themselves buried every generation or so. The standard remedy is to just build another level on top, so now the city descends through the earth to an unknown depth. This has caused friction between the dwarfs, who traditionally view anything underground as theirs, and the city's government, who think of those areas as sub-sub-basements and would rather not have unknown factors tunneling through them.
 * Also from Discworld, the mine-city of the Low King of the Dwarfs is built mostly under the surface town of Bonk.
 * Inverted in CS Lewis's The Silver Chair. The thriving kingdom of the Lady of the Green Kirtle is underneath the ruined city of the giants., which is abandoned but not for long.
 * In A Darkness at Sethanon, the titular Sethanon was built right on top of an ancient Valheru city.
 * In Isaac Asimov's short story "Nightfall," archaeologists discover that a hill near their city is actually the ruins of several older cities, piled on top of each other. They all burned down at suspiciously regular intervals.
 * In the Doctor Who New Adventures, there's the Undercity of Spaceport Overcity Five -- or, as we would say, London. In this case, London wasn't buried: the entire Overcity floats above it on Anti Gravity engines.

Live Action TV

 * Cities of the Underworld is a documentary series that aired on the History Channel and explored subterranean structures under various cities and historic sites around the world.

Tabletop Games

 * Dungeons and Dragons. Judges Guild module Dark Tower. In the Backstory, a small village grew up around the White Tower of Mitra. When the Black Tower of Set appeared nearby, the village was buried by the landslides caused by the battle between the two towers. Within a decade a new village of treasure seekers called Mitras's Fist was established on the ground where the old village had stood. When the new villagers began digging down to find the old village, imagine their surprise when they found someone digging up to meet them...
 * Cities in Warhammer 40000 almost invariably have such an "undercity". They're considered the natural consequence of being established for as long as any WH40K city.
 * Forgotten Realms has cities built this way, particularly big and old ones like Westgate. In another way, Waterdeep stands on the still active Undermountain complex and Skullport city and Ravens Bluff stands above an abandoned dwarven city under which there's in turn an abandoned drow city.
 * Dark Dungeon RPG, supplement Samaris, Island of Adventure. At one time the entire island of Samaris was covered by a giant city, which was also called Samaris. The city was destroyed in a war between the North (led by the demonic wizard king Acecerax) and the South (led by the demon witch empress Vekna) two hundred years ago. Southport (the largest city on the island), Northport, Eastport, Westport and Zentrumstadt are smaller cities built upon its ruins.

Toys

 * Metru Nui in Bionicle, under the island of Mata Nui.

Video Games

 * Old Mournhold in The Elder Scrolls 3: Tribunal.
 * Saints Row 2 has Old Stilwater, an earthquake-ruined underground district from approximately 1940-1965, inhabited by hobos, accessed by entering the old mission house.
 * The Undercity in Baldurs Gate is an ancient settlement located in a cave underneath the eponymous city. It is apparently big enough to house an enormous temple of Bhaal and many supporting structures.
 * Paper Mario the Thousand Year Door has the ancient city buried under Rogueport.
 * The Lost City in Thief game series.
 * Wonder City in Batman Arkham City.
 * Blackreach in The Elder Scrolls V Skyrim, former capital of the Dwarven lands.
 * Vagrant Story has an Undercity area, notable for its high density population of undead.
 * In Pokémon Colosseum, there is another city buried underneath Pyrite Town, known simply as "The Under". It is actually a full city (complete with shops, an inn, and fighting arena), rather than being just abandoned ruins and buildings.
 * Old Ironforge, located under the dwarven capital Ironforge in World of Warcraft.
 * Also in World of Warcraft, a literal inversion: the Undercity is the capital of the undead race the Forsaken, while the old city of Lorderon above it is the mostly-abandoned ruins.
 * in Torchlight, you explore a stack of these, many layers deep.

Western Animation

 * Teenage Mutant Ninja Turtles 2003 has a lost alien city below New York, as well as a rotting system of abandoned mining tunnels where some of The Shredder's mutates lived.
 * In Avatar: The Last Airbender, Old Ba Sing Se is buried under Ba Sing Se.
 * Old New York in Futurama.

Real Life

 * Moscow has a lot of Soviet-era underground works, partly civilian (Metro) but mostly of Cold War era Soviet military origin. Urban legends tell about a whole system of special Metro for the government and underground vault-cities in case of a nuclear war, for generals and officers.
 * Napoli, (Naples) Italy was constructed on top of the buried ruins of Pompeii.
 * Underground Seattle. This was a part of the late 19th century Seattle business district that was buried when the streets were regraded.
 * Mexico City is built on top of the ancient Aztec capital of Tenochtitlan.
 * Many old European cities like Rome or Paris have catacombs beneath them.
 * Link to relevent page on The Other Wiki.