Primordial Chaos

In Plato's Timaeus, God does not create the universe, as does the Christian God; He simply finds it one day. It is in a state of total chaos. God sets to work to transform the chaos into order.

—Philip K. Dick, describing a classic example of this.

In almost all mythologies, there exists a time before time, where the world had not yet been made. All that existed was simply Chaos (usually), and from here the gods/primordial entities would form, and shape the world as they saw fit. In other cases, there was nothing at all, and in others still, it was someplace indescribable by mortal words. It may still exist in some form, either as a (strange) part of the reality in question, or as a connected but separate reality.

Eldritch Abominations like to call this place home. It occasionally has an Anthropomorphic Personification, or may be sentient itself. It's also nearly always part of a Creation Myth. Sometimes it's the site, or result, of a War in Heaven.

The Cosmic Egg may have resided in it.

Examples of Primordial Chaos include:

Anime and Manga

Slayers has the Sea of Chaos, from which the four worlds arose at the beginning of time.

Comics

Marvel Comics villain the Chaos King is the Primordial Chaos as an Anthropomorphic Personification. He's very loosely based on the Japanese mythological figure Amatsu-Mikaboshi.
In Alan Moore's Swamp Thing, during a tie-in to Crisis on Infinite Earths, a Complete Monster cult called the Brujeria summons up something far, far worse than the Anti-Monitor: this very chaos, called the "Original Darkness." It's likely the most powerful supervillain DC has ever thought up: its fingernail couldn't be dented by The Spectre, and, again, this is during Crisis, meaning this is the same Spectre who fought evenly with the Anti-Monitor after the latter had absorbed the Infinite Earths. Despite its power, however, the Darkness is a rather innocent being, very ignorant of the ways of the universe. It absorbs Etrigan, Doctor Fate, and the Spectre, trying to get information from them, but they just end up making it worse when they tell the Darkness that it is "evil." Swamp Thing then convinces it that it is what it makes of itself, and finally the Presence Himself descends from Heaven and merges with the Darkness, equalizing it.
Over twenty years later, during Blackest Night, the origin of the Green Lantern villain Nekron is given: it turns out he is a "defense mechanism" created by the Primordial Chaos to fight back against light and life. You see, the universe rightfully belonged to the Darkness; the Presence invaded when He created the Entity, which in turn created life. Whether this Darkness is the same being as the Swamp Thing character is anyone's guess, but given Geoff Johns' apparent fondness for Alan Moore stories about Eldritch Abominations, it wouldn't be surprising.

Literature

The Silmarillion starts this way. God (Eru) creates classes of angels (Ainur), then shows him his grand design (through having them sing), and sends them out into the void to create it for him.
In the Discworld series, the Anthropomorphic Personification of kaos (none of this new mathematically-defined chaos, thank you very much) used to be the fifth horseman of the Apocalypse. The other four threw him out for being overly destructive, and now he runs a dairy as Ronnie Soak, Milkman.
In Steven Brust's To Reign in Hell, Yaweh and the Angels are fighting to save Heaven from incursions of the formless, chaotic, destructive Cacoastrum from which they all originally sprang.
The substance called "nothing" in Garth Nix's The Keys to The Kingdom books.
In the Cthulhu Mythos, Azathoth is described as this. As Lovecraft wrote: "the ancient legends of Ultimate Chaos, at whose center sprawls the blind idiot god Azathoth, Lord of All Things, encircled by his flopping horde of mindless and amorphous dancers, and lulled by the thin monotonous piping of a demonic flute held in nameless paws." Ramsey Campbell makes Azathoth an inversion: as it wasn't always ultimate chaos. It became that way when it lost it's intellect.

They danced insanely to the high, thin whining
Of a cracked flute clutched in a monstrous paw,
Whence flow the aimless waves whose chance combining
Gives each frail cosmos its eternal law.

In the Young Wizards series there is Eternity, the place outside of time where the Powers That Be dwelled before they created the universes. The most powerful of the Powers still exist mainly in Eternity, projecting mere fragments of themselves into the universes to interact with things that exists inside of time.
The Other Place in "The Bartimaeus Trilogy".
The Warren of Chaos in The Malazan Book of the Fallen.

Mythology and Religion

Greek Mythology has... well, chaos.
The sea of nothingness known as Apsu in Mesopotamian Mythology is the Ur Example.
The Bible says that in the beginning, the Earth was formless, empty, and covered in darkness.
- Interestingly, sea still seems to exist, as it mentions how the spirit of God moved over waters before any creation had taken place. Anthropologists have suggested that nothing spoke "chaos" as well to a tribe of desert nomads than a raging sea.
Ginnungagap in Norse Mythology was the void between the unbearably hot Muspellheim and the bitterly cold Niflheim in which the world emerged.
Japanese Mythology describes the "primordial chaos" from which the Gods came from (and created the Heavenly Plains and later Earth) as dark, cold and jelly-like. The Star God Amatsu Migaboshi Is usually associated to the pre-Earth chaos.
Hindu Mythology. In fact, gods even intentionally fished there once, just to see what they will pull out of it. And collected an impressive pile of weird stuff, some more useful than other. No boots, though.

Tabletop Games

Exalted has the Wyld, which still exists around creation and periodically tries to eat it. It's also home to The Fair Folk.
In Legend of the Five Rings, one of the villains, responsible for "real" ninjas is this - leftovers of the primal darkness, which hate being forced into shape and so would like to undo all creation. The ninja powers of its servants comes form them being "unnamed" - they don't have true names and as such aren't set in reality - their shape is a matter of whim.
Warhammer 40,000 has the Warp.

Video Games

Zelda: Ocarina of Time: "Three golden goddesses descended upon the chaos that was Hyrule..."

Real Life

Under some hypothesis, the Big Bang arose from a pre-universe described as a "Quantum Foam".
Another hypothesis says nothing existed, because before the Big Bang time didn't exist.
- This idea has lost credibility in the eyes of most physicists, both because of the logical conundrum it presents (if there is no time, nothing can "start" in the first place) and because it relies on the rather narrow definition of "time" to begin with, as the entropic constant rather than the fourth dimension.