Sunken City

One of the easiest ways to indicate that a major, Earth-changing event has taken place is to show a city half-sunken, with buildings at unsafe and possibly nausea-inducing cants. This is sometimes the result of a Green Aesop about Hollywood Global Warming, but more often it's just used to show that something is not right in the story's setting.

Given the natural fears that arise in an island nation, this happens to Japan a lot.

Anime and Manga

 * Tokyo in Ghost in the Shell.
 * Tokyo in Neon Genesis Evangelion.
 * Blue Submarine 6
 * Yokohama Kaidashi Kikou
 * Ponyo on the Cliff by the Sea (in a strangely lighthearted way)
 * The nameless ruined city in El-Hazard: The Magnificent World used to showcase the ancient destructive power of the demoness Ifurita.

Film

 * New York in AI
 * New York in The Day After Tomorrow

Literature

 * The 1987 novel Drowning Towers (or The Sea and the Summer) by George Turner describes a future in which Melbourne was partially submerged in water. As the tops of sky scrapers are above the water level, they are still inhabited by the cities' poorer classes.

Video Games

 * Sunken City (possibly the Trope Namer) in The Legend of Zelda Oracle of Seasons, flooded not by rising seawater (it's quite far from the ocean) but by melting snow from the mountains.
 * Many of the Post Apocalyptic alternate earths one could reach via Portal Corp in City of Heroes were basically ruined buildings surrounded by water, although with a bit more dry land at their feet than is usual for a truly "sunken" city.

Western Animation

 * Atlanta in Futurama, Played for Laughs of course. "The Lost City of Atlanta!"
 * In an episode of Captain Planet, the characters go forward in time and see New York underwater. And yes, it was a Green Aesop about Hollywood Global Warming.