"All wars are Civil Wars, because all men are brothers."
— Francois Fenelon
A Civil War is an intense conflict between organized groups trying to take control of a state and/or region, or to change government policies. Most Civil Wars are fought by a status-quo ruling body of the state and one or more groups that wish to change said state, though said non-state groups often fight each other as well, and it can also be between two states that both claim to be the sole rightful (nation-)state for a single nation. To be considered a "war" rather that an uprising or rebellion requires that the conflict involve regular armed force, involve organized factions, and be on a certain scale and of a certain intensity. All the sides involved have to have a genuine chance (however small) of achieving their aims in the conflict for it to be a Civil War and not just a rebellion/uprising. Where rebellions end and Civil Wars begin often isn't clear, and whether a conflict is called one or the other often depends on what the factions - especially the victorious one - decide to call it.
Those fighting Civil Wars usually don't call them that, as they try to make use of the power of language to suggest that they are in the right: the ruling power will term it it as an action against a dangerous uprising by crazed rebels. Said rebels will consider themselves Freedom Fighters against an overbearing ruling class. However, it is just as likely for a small group of rebels to claim Civil War status (as such terminology would give their actions an air of legitimacy it would not otherwise have), or likewise, for the government to use the term (to justify force that would seem excessive against a mere criminal action). How the outside world views the situation is largely Written by the Winners. This is largely why wars for independence are so murky when it concerns the concept: generally, if a country fails to gain independence, expect it to be called a civil war, and if it does, expect it to not be so termed.
No matter who prevails, it is often a Pyrrhic Victory, as, depending on the world situation, internal conflict provides a ripe opportunity for conquest by another nation: Divide and Conquer if the villain takes advantage, and Enemy Civil War for the heroes.
Civil Wars both real and fictional have provided excellent opportunities for stories, as depicted morality can be all over the board. The fact that both sides believe themselves to be justified allows for an authorial portrayal of both sides having good people fighting for what they believe in along with a couple of real bastards on both sides. Often, while one side may indeed be presented as morally superior, there will be a Worthy Opponent among the enemy ranks and the Perspective Flip is common. Along with that, there can be Star-Crossed Lovers pining for each other across the battlefield and families split by the tension of what they believe is right.
Many an Alternate History is based around one side of a Civil War prevailing over another.
This is not to be confused with Marvel Comics' Civil War.
Examples of factual Civil Wars commonly used in media:
The American Revolution (1775-1783), a conflict in which France, Spain, and the Dutch Republic backed British rebels to check growing British power, leading to the formation of the United States of America.
The Galactic Civil War within the Galactic Empire forms the central conflict of the Star Wars franchise, preceded by the Clone Wars, fought between the Galactic Republic and a Confederation formed for seceding Republic planets. Numerous smaller-scale civil wars are noted in the Star Wars Expanded Universe, and initially the Empire cracked down on them fiercely, unlike the Republic which usually let them be or sent Jedi to figure things out. Later the Empire was content to let them rage while chasing Rebels.
A civil war is an important part of the backstory in A Brother's Price. The royal family of Queensland had such a wealth of daughters that the family was split, the older half staying and marrying Michael, the younger half marrying Raphael and moving to rule recently-annexed Southland. But Michael turned out to be infertile, and the younger sisters became more and more insistent that their children be considered the heirs. This led eventually to what was called the War of the False Eldest, which ended with all of the younger sisters and their children being executed. Except, it turned out, for their boy Alannon, who was abducted by Queensland spies; he is dead by the time of the book, but the Royal Blood he passed on certainly has an impact on his grandson.
Most of A Song of Ice and Fire is devoted to this. They start calling it The War of the Five Kings in the second or third book. In the Back Story there are more, such as the Dance of the Dragons, the Blackfyre Rebellion and Robert's Rebellion.
Discworld's Ankh-Morpork has a number of Civil Wars in its backstory, though the narrator makes clear that many were accidental, overblown in the retelling, and generally not very competent affairs. It is mentioned that while the Patrician, Lord Vetinari, has created a time of relative peace under his rule, he has done so by playing increasingly small factions against each other, to the point where, although everyone is technically still fighting a civil war, no one can do enough damage or make enough money out of it to become a threat. The Night Watch books in particular utilize the concept.
The Wizarding Wars of Harry Potter. Presumably Voldemort had his eye on global conquest, but the books focus on his attempts to fully consolidate power in Britain, and those fighting against him from within.
Two of them on Babylon 5: The Earth Alliance Civil War, and later the Minbari Civil War. Several other civil wars are indicated or implied to happen off-screen after the show's end, such as the Telepath War on Earth and Vir's rebellion against Emperor Londo Molari on Centauri Prime.
The fight of the Federation against the Maquis in the Star Trek franchise veers from this to portraying them as merely a terrorist group, Depending on the Writer.
Supernatural season six involves a civil war in Heaven, as the Council of Angels fragments after season five's Screw Destiny ending. On one side, Archangel Raphael and those who think the Apocalypse should be restarted. On the other, Castiel and those he's convinced to try this "free will" thing. There's plenty of spillover onto Earth, although most of it is left to our imagination. It gets so bad Castiel is willing to work with Crowley, then give up on free will altogether and declare himself the new God after absorbing the souls of Purgatory. This ends badly.
The Horus Heresy is one of the biggest setting-defining events of Warhammer 40,000, despite the fact it took place ten thousand years ago in the past.
Happens frequently in BattleTech. The Free Worlds League tend to be at civil war with each other from time to time, and the Clans don't always agree with one another and fight each other just as often during their Invasion. Then there was the FedCom civil war instigated by Katherine Steiner-Davion for control over two states.
The Empire is trying to hold onto Skyrim because it needs both the resources and the manpower, especially since they expect a full-scale war with the Aldmeri Dominion in the future. Skyrim also acts as a vital transportation hub, connecting the heart of the Empire to all of its other territories. While the Empire is criticised for not understanding the people of Skyrim or their cultures, they are generally considered fair and just rulers by the common citizens. However, the Empire's vast bureaucracy and weak leadership clog their government with inefficiency.
The Stormcloaks view the Empire as an oppressive foreign power that is weak and unfit to rule Skyrim, and are violently opposed to the Empire's ban on the worship of the human god Talos (a clause that was reluctantly added to the peace treaty the Empire signed with the Thalmor). However, the Stormcloaks carry a noticeable degree of Fantastic Racism against non-Nord races, and their rebellion is perceived by many as ill-timed and short-sighted, especially in the face of the true threat of the Thalmor.
The entire war was instigated by the Aldmeri Dominion. The Thalmor's intent was to soften up the Empire for another invasion attempt, though they realize they may have underestimated Ulfric. The Dragonborn getting involved and quickly ending the war in favor of either side will completely derail this plan since it means the Thalmor will either have to face a united Empire or a two front conflict against the Empire and Skyrim. The only truly "wrong" choice for the Dragonborn is to do nothing.
In Mass Effect 3, the Robot War between Quarians and the Geth was actually spawned by a Civil War between Quarians who sympathized with the Geth and Quarians who wanted to destroy them all. The Geth only took up arms to defend their friends, but this eventually became "defend themselves" when the quarian sympathizers were rendered into a non-entity.
In Transformers in general, the default state of Cybertron seems to be a state of civil war to provide a reason for robots to shoot each other. There have also been various internal conflicts within both Autobot and Decepticon, and occasionally Maximal, Predacon, and Vehicon ranks.
Book 2 of The Legend Of Korra looks to be about one between the Northern and Southern Water Tribes.