The Great Flood

What happens when God (or the gods) decides to Kill It with Water. All of it.

Older than the book itself, this is the one element that seems nearly ubiquitous in mythology, and with good reason: it may have had a basis in reality (a hypothesized late Pleistocene/Early Holocene flooding event, possibly from a small asteroid impact or earthquake off the coast of Madagascar causing a tsunami), but as a kind of cultural memory it forms the backbone of many origin mythologies, from the Australian Aboriginal Dreamtime to the biblical Book of Genesis. Usually the moral of the story is "don't piss off the gods," but sometimes the flooding is part of the process of (re)creating a world.

Some scientists argue that the prevalence of the Great Flood in Eastern Mediterranean myth derives from a historical event, in which the Black Sea was suddenly flooded in about 5600 BCE. Others point to evidence of an asteroid or comet impact in the Indian Ocean, which could have sent tsunamis well over a kilometer tall miles inland throughout the Middle East, Africa and southern Asia. Either way, this would only account for the myths from those specific regions, not the ones from the rest of the world. And, of course, some of various religious persuasions believe that the prevalence of the Great Flood myth derives from an actual worldwide great flood caused by their deity of choice (although a global flood isn't plausible by mainstream science).

Examples of The Great Flood include:

Mythology and Religion

The Bible, obviously. Noah lives.
- Averted in the Qur'an, in which the flood is merely local and destroys only one civilization.
The Epic of Gilgamesh: The earliest recorded example.
Gnosticism subverts this trope, as it does so many. Noah constructed the ark according to the instruction of the malevolent Demiurge, but it was burned down with magical fire by Eve's daughter Norea in a fit of supernatural rage. He built a second ark, which turned out to be useless because they were just transferred temporarily into Heaven for the length of the flood.
Various Native American Mythologies
Various Asia-Pacific and Polynesian Mythologies
~~Greek~~ Classical Mythology has three, most notably Deucalion's.
This list could go on forever. Just check The Other Wiki: Flood myth.
According to Plato, Atlantis was actually destroyed by a giant tidal wave known as the "Mebhelmok" (which actually means "great flood").
Norse Mythology. Ymir is killed and his blood flooded the earth and drowned all but two of the frost giants.
Hindu Mythology: The earth sank into the sea for some reason and Vishnu, as the Boar Avatar, went down and brought it back to the surface.

Anime and Manga

Saint Seiya: the god Poseidon, wishing to wash away the filth of mankind, raises the oceans to destroy all of civilization. In the anime, this is compounded by the priestess Hilda praying to Odin to preserve the ice in the Grim Up North eternally frozen; her absence causes it to melt and contribute to the flooding. Confusingly, this (and the first major story arc) is all part of a Xanatos Roulette that started long before the start of the series.
Dragon Knights: the demon fish Varawoo sunk the world before it was sealed away.
Now and Then, Here and There : Don't piss off Lala Ru.

Film

This was the end result in 2012. The earthquakes and volcanic eruptions were merely a prelude.
The "Rite of Spring" segment of Fantasia actually ends with the entire Earth being flooded by a massive tidal wave caused by a solar eclipse.
In Atlantis: The Lost Empire the Biblical flood was caused by the Atlantis' weapons research and the city was sunk to save it from destruction.

Literature

Raptor Red: A flood of the sort that only comes every thousand years strikes Raptor Red and her family around the middle of the story.
In Shane Johnson's Ice an astronaut ends up traveling back in time where he experiences the biblical flood.
Flood, by Stephen Baxter, is a hard sci-fi depiction of a global flood in modern times.
One of the two founding myths of Discworld's Ankh-Morpork involves a boat that was built to withstand a great flood, containing two of every animal. The accumulated waste products of all the animals was tipped over the side, and they called it Ankh-Morpork.
- In Carpe Jugulum, one of the things that worries the Slightly Reverend Mightily Oats about Omnian dogma is that every Discly culture has a flood myth, similar but different to the one in the Book of Om.
According to Word of God, the past of the Septimus Heap universe featured one, causing Syren Island to sink beneath the sea.

Live-Action TV

The 2000s Battlestar Galactica: Gaius Baltar mentions the story of the Flood as explained in the Book of Phytia to Roslin, comparing his role in the destruction of the Colonies to that of the Flood. While no actual Flood is seen, the story is clearly a reference to the biblical story and may even have been its origin.

Video Games

Perfect Chaos from Sonic Adventure.
One of these apparently happened sometime between Mega Man ZX and Legends.
The Legend of Zelda: The Wind Waker takes place in a world where the Flood waters have yet to recede. Everybody lives on mountaintops.
In Final Fantasy III, destroying the balance between Light and Darkness plunges the world into the latter, freezing the surface in time and then flooding it so only a temple and a priestess remain above water.
The goal of Team Aqua in Pokémon Ruby and Sapphire and Emerald.
Killing Poseidon unleashes a great flood in God of War 3. And he's merely the first God to die in that game.
Konami's Noah's Ark actually takes place during the flood where the water slowly raises during gameplay.
Fire Emblem: Radiant Dawn explains that before years began to be counted, Ashunera expressed great grief over the warring of the Beorc and Laguz, and caused the entire world to be flooded due to her grief overlapping with her power unintentionally. She then split into Ashera and Yune, causing a war of dominance to take place.

Real Life

The Boxing Day Tsunami.
The 2011 Australia floods.
A number of record-breaking floods throughout recorded history could be considered as these, at least in terms of regional and economic effects.