Part of the reason why this trope is so pervasive has to do with the history of the airship, starting with World War I. During that war, Germany used Zeppelins as bombers against Britain and France, and although they did relatively little damage they terrified Allied civilians. After the war, zeppelins were used as passenger carriers by Nazi Germany up until 1937. On the civilian side, blimps are often used for advertising, which ties into fears of power-hungry CEOS with massive egos.
Another reason for this is that airships just look intimidating, in a way that airplanes and helicopters don't. Their massive size and slow, silent flight give them an ominous air, which naturally makes many writers and filmmakers fix upon them as vehicles for fictional bad guys.
Thus the airship became the go-to flying transport for all manner of fictional dictators, warlords, Sky Pirates, and other miscreants. This trope applies not only to airships in the real-world definition (powered lighter-than-air aircraft) but also to fictional vehicles that are called "airships" but use other means of lift, as are often found in Steampunk settings. It can, but need not, overlap with Cool Airship and Zeppelins from Another World.
A couple notes before adding examples: If airships are used by both heroes and villains in a story, that's not this trope. If a villain uses an airship at some point, but it's not particularly significant or otherwise associated with them, that's also not this trope. However, if airships are clearly associated with villains in the setting, that's this trope.
- The thieves' airship in The Daughter of Twenty Faces.
- Lawrence III's airship Hikoukyu (Japanese for "Flying Palace") from Pokémon 2000 and Zero's Megarig from Pokémon: Giratina and the Sky Warrior
- In Pokémon Adventures, there's the Team Rocket Airship in the FireRed/LeafGreen arc that can turn into a stadium with a push of a button. Giovanni probably designed it that way specifically for his rematch with Red.
- And Team Rockets' Meowth-shaped hot air balloon, which just happens to be their main form of transportation. However, after they Took a Level in Badass in the Best Wishes anime, they abandoned the Meowth balloon and replaced it with a simple purple hot air balloon with a stylized Team Rocket "R" insignia on it.
- In the Diamond and Pearl series, we have Hunter J's airship; quite appropriate for arguably the biggest Knight of Cerebus of the anime.
- Hellywood from Now and Then, Here and There is a prime example of this trope. We don't actually see it fly until the 10th episode of the show, though. But when it does, it's quite a sight— it is, for all intents and purposes, a flying skyscraper with a built-in Wave Motion Gun.
- Hellsing: Has the Millennium's airships, which are used to conduct the attacks on both London and the Hellsing Organization Headquarters, and are loaded with Nazi Vampires.
- Batman Black and White: The climax of "Heroes", set in 1937, features a Nazi airship.
- In The League of Extraordinary Gentlemen, Professor Moriarty and Fu Manchu set out to attack Victorian London with their cavorite-powered Cool Airships. The page image shows Moriarty's ship (which is the only one of the two that actually sees action due to Moriarty stealing the cavorite).
- In the Elseworld miniseries Marvel 1602: Fantastick Four, Otto Von Doom has an airship that is literally a sailing ship with a balloon over the top. He uses it to kidnap William Shakespeare.
- Dungeon Keeper Ami: Ami's airships are a new technology to the people she shows it to, and her occupation is basically only comprised of evil people, except her, but they don't know that.
- In The Great Mouse Detective, Big Bad Ratigan has a sinister-looking blimp with sharp, flaring metal tailfins... driven by a pedal-powered propeller and rudder.
- Atlantis: The Lost Empire has the Gyro-Evac, essentially a cross between an Escape Pod and a hot-air balloon — shaped like a rocket and designed to go straight up very quickly, armed with gravity bombs and hidden in a tanker truck until the true villains of the movie reveal themselves and their plot to abscond back to the surface with the lost treasures of Atlantis.
- Up: Charles Muntz's cold, grey, massive zeppelin contrasts with Carl's small, colorful balloon-propelled house. Carl gets to keep the airship in the end, though.
- Max Zorin's airship from A View to a Kill may look like a boring old blimp, but does yours unfold from a construction shack and come with an integrated deathtrap? Max even gets to make a Bond One-Liner.
- In The Three Musketeers (2011), Cardinal Richelieu's forces get a huge airship (based on an in-universe design by Leonardo da Vinci) near the end of the film and use it to combat the one that the musketeers had hijacked.
- The climax of The Rocketeer takes place high above Hollywood aboard the Nazi dirigible Luxembourg. While it doesn't exactly belong to the Big Bad, movie star and secret Nazi spy Neville Sinclair, it's all part of a plot based on intelligence Sinclair provided, and he does dramatically leap from the burning airship after stealing the title character's rocket pack... at which point a leak in the fuel tank causes him to crash into the Hollywoodland sign and explode.
- Doctor Who combines this with Zeppelins from Another World in "Rise of the Cybermen". The TARDIS crashes into an alternate history, where airships are still in common use in the modern day. Specifically, they're used by Cybus Industries, an amoral corporation that sees its customer base as research material and eventually creates the Cybermen in this version of the show's continuity.
- "Airlords of the Ozarks", an adventure for Twilight: 2000, had the players, having returned to the U.S.A., recruited to investigate what turned out to be a neo-fascist movement using airships for raids to build a power base.
- Call of Cthulhu: supplement Fearful Passages, adventure "Rigid Air". The dirigible Bellinghausen (AKA Terra Nova) and part of its crew have been taken over by a Cthulhu Mythos entity called a dho-spawn. The dho-spawn has spent months tracking down and decapitating ex-members of the crew. The Investigators must discover the truth and destroy the dho-spawn before it perpetrates more evil.
- Airships are a recurring vehicle of choice for Bowser and his Koopalings across the Super Mario Bros. series, and are typically used as siege weapons when Bowser tries to take over the Mushroom Kingdom or kidnap Princess Peach. As a general rule of thumb, if boss levels in the 2D games (at least the ones since they were introduced in Super Mario Bros. 3) don't take place in a castle or fortress, they're typically on an airship. For reasons unknown, the Mushroom Kingdom is rarely seen using air travel of their own, though Mario has piloted a Cool Starship in Super Mario Galaxy 2 and a souped-up hot-air balloon in Super Mario Odyssey, and Mario, Peach, and (sometimes) Luigi have been seen occasionally riding in much smaller, unarmed hot air balloons (and in at least one instance, a conventional modern-day airplane) in the prologue or epilogue of a handful of games,
- In Warcraft II, Goblin Zeppelins were The Horde's equivalent to the Gnomish Flying Machine. This is averted in future installments - goblins became a neutral race in Warcraft III and early World of Warcraft, and when they re-joined the Horde, they weren't an evil faction anymore.
- The second and third installments of the Command and Conquer: Red Alert series give the Soviet faction the Kirov Airship heavy-bomber rigid/semirigids. While the Soviets aren't always evil in 2 and 3, with their villainy mostly being Played for Laughs, they do tend to be the "bad guys".
- Sonic the Hedgehog: Dr. Eggman loves building flying battleships. He had the Wing Fortress in Sonic the Hedgehog 2, the Flying Battery in Sonic 3 & Knuckles, the Sky Fortress in Sonic the Hedgehog 4, the Egg Carrier (and backup Egg Carrier 2) in Sonic Adventure, and more. In chronologically later games, such as Sonic Heroes, he has an entire fleet of airships.
- In Syndicate, the Villain Protagonist was calling the shots from his personal airship. If you lost all your agents, you got a cutscene of the Syndicate destroying it with a bomb.
- CarnEvil: Ludwig von Tokkentakker, the Big Bad, has a giant zeppelin-like airship perched on top of the Big Top, the final level. Tokkentakker brings you on board the airship for the final battle.
- Henry Stickmin Series: The Toppat Gang has one. It is primarily featured in Infiltrating the Airship, and also shows up in one ending of Fleeing the Complex.
- Bravely Default: the Sky Knights fly a giant zeppelin. Though unlike other examples, they style themselves as heroic defenders, despite actually just being thugs abusing their power for their own ends.
- The primary enemies of the Bloons Tower Defense series are the Bloons. While regular ones look like balloons, the strongest ones resemble blimps. The blimps move slowly, but they're much tougher and are generally more resistant to slow and stun effects.
- In Avatar: The Last Airbender, one of the war vehicles the Mechanist made for the Fire Nation was a hot air balloon. It ended up being used against the Fire Nation, but they found its wreckage and reverse-engineered it to make war zeppelins. They use them to devastating effect on the Day of Black Sun to compensate for the loss of firebending. In the series finale, Ozai takes a fleet of zeppelin and comet-boosted firebenders to start burning the Earth Kingdom to the ground.
- TaleSpin: Don Karnage and his Sky Pirates operate out of the Iron Vulture, a cross between an airship and an Airborne Aircraft Carrier.
- ''Action Man (2000): Dr. X and his Council of Doom have a high tech airship that, among other things, can turn invisible. It originally belonged to Tempest, who used it to control the weather in his debute episode, but Dr. X made it his headquarters after accepting Tempest into the council.
- The Hawk from the Josie and the Pussycats episode "Melody Memory Mix-Up" is a villain prowling the skies in a dirigible. He's seeking Professor Layton's force field plans in order to make his dirigible impervious to anti-aircraft weaponry. From this impregnable flying fortress, Hawk aims to monopolize air traffic lanes and demand ransom to allow passage.
- In DuckTales (2017), Don Karnage returns from TaleSpin with an Iron Vulture that serves as an airship as well as a carrier for fighters. When Glomgold unites the villains in "GlomTales!," it becomes the de facto headquarters for his Legion of Doom.
- PJ Masks: In Season 3, Romeo gets his own flying headquarters called the Sky Factory.