Last Bastion

It's all gone. They're all dead. Only this one fortress remains against our impending doom -- the Last Bastion. From here we can wage our war, stage guerilla attacks, or send a small, but elite strike team to hit where it hurts most. If we buy enough time, we might even be able to get our hands on that one thing that can save us, and maybe, just maybe we can win. But if that fails, we can at least go down fighting. That is, assuming we can fight back at all....

Compare the Undefeatable Little Village.

Anime and Manga

 * NieR:
 * In MD Geist 2:Death Force, MD Krauser's armed fortress is the only safe place against the horde of flesh-eating robots that have ruined the planet.
 * The Macross in Robotech after Earth gets shitcanned.
 * Tsubasa: Reservoir Chronicle: In volume 15, the Tochou building

Film

 * The Matrix : Zion, home of the last free humans and party scenes that are way too long.
 * Fiddlers Green in Land of the Dead
 * The prison in Resident Evil: Extinction.

Literature

 * Eragon : Farthen Dur
 * The Lord of the Rings: Helm's Deep serves this exact function for the Rohirrim.
 * Minas Tirith during Sauron's attack in The Return of the King.
 * The underground military research facility in Robert A. Heinlein's Sixth Column.
 * The Last Redoubt in William Hope Hodgson's The Night Land. During the course of the novel another, forgotten Lesser Redoubt is discovered.

Live-Action TV

 * In the Supernatural Flash Forward episode "The End" Dean meets Future!Dean, who leads a small group of rebs based in a camp in the woods.

Tabletop Games

 * Dungeons and Dragons module Q1 Queen of the Demonweb Pits. The fortress of Kandelspire is the only thing that stands in the way of Lolth's invasion of the dwarven kingdom of Maldev.

Video Games

 * Legacy of Kain: Soul Reaver: The Human Citadel.
 * Mega Man Zero: The aptly and creatively named Resistance Base.
 * System Shock: In the first game, the survivors are holed up in a room in Beta Quadrant of the Medical Level.
 * Jacinto in Gears of War
 * The Valais Air Base in Ace Combat Zero is the last Allied stronghold that has not fallen to the Belkans yet. Naturally, your job is to bring the Allies Back From the Brink.
 * In Fire Emblem: Seisen no Keifu, the Foreteress of Darna was this to the original Liberation Army, until the gods appeared to them and gave immense powers to the 12 Crusaders, allowing them to fight back and win against the Lopto Empire.
 * The Ark in Halo 3.
 * Reach in Halo: Reach. Oh, wait.
 * Bastion. Naturally. In an interesting subversion, the game remains mostly light throughout. There is no active threat or advancing army,  and you're free to take your time and explore, even just before the final area.
 * Praetoria in City of Heroes is the last surviving human city in a version of Earth overrun by monsters. It's made out by its ruling class to be the proud (and successful) resistance to their attempts to kill all humans.

Web Comics

 * In Homestuck, the trolls manage to escape from the demon that's destroying their session by hiding on a meteor in the Veil - which is a giant cluster of meteors. While it was depleted by the Reckoning, they were safe enough that.

Western Animation

 * In The Simpsons Treehouse of Horror story "Don't have a Cow, Mankind" there's a Safe Zone outside the city.

Real Life

 * During the last months of the Russian Civil War, Crimea was seen as this by the White command who were still planning some Back From the Brink.
 * During World War II, the Germans had a massive stronghold called the Alpine Fortress, which was constructed in the mountainous areas of southern Germany. It was built with the idea that if Germany were overrun, top Nazi officials, their staffs, and a large number of crack troops could retreat there and, with a stockpile of supplies and some limited production facilities, continue to harass the Allies for many years to come. However, the Fortress was far from impregnable by the time it became needed and it was taken easily shortly before the Berlin occupation. Even so, reports of its staggering defensive strength were partially responsible for the Allies' broad front strategy to take the southern regions and the Fortress before moving onto Berlin, rather than the narrow charge advocated by General Patton.
 * Switzerland has a massive fortification system called the National Redoubt. Put to use during World War II, the National Redoubt had a series of forts, cannon positions, and other fixed defenses throughout the Swiss Alps. The Swiss battle plan in case of invasion, which was no secret, was to fight a holding battle in the lowlands for as long as possible, and then pull back to the Redoubt. The fortifications also commanded Switzerland's many passes and tunnels connecting Germany, France, and Italy; any attempt at invasion would mean cutting off that vital traffic. After the war, the defenses were examined and found to have more and better cannons than both the Maginot and Siegfried Lines combined.