Some villains have their own country, and with a desolate volcanic wasteland around their tower that the heroes must battle their way through. Others, however, have bigger plans. Entire solar system, maybe. Alternate universe, perhaps. And right in the middle is this place, a floating castle of doom overlooking — well, pretty much nothing. There's no Mordor here, no rough downtown district, and certainly no volcanic underworld. The base floats in absolute nothingness.
On top of that, there are multiple versions with their respective associations. A Floating Continent with this place on top will often be a rather mystical area, while various space-faring series usually have an enormous battleship in the centre or edge of the universe for the alien invaders. Then, of course, anything literally in a void has a pretty good chance of being a Mind Screw. Nevertheless, it's relatively common, especially as a Very Definitely Final Dungeon in a videogame, providing the backdrop for many an extremely powerful evil force.
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In a Void of Nothingness
The preserve of extremely destructive, powerful and unhinged villains, these places literally have nothing around them. Often located in Another Dimension, they're infinite, gloomy, and depressing places which would drive most characters completely insane. May well vanish altogether after being completed.
In Astro City, Infidel lives in such a palace. It's actually something of a prison, though one he resides in voluntarily.
Prometheus, a Justice League of America villain, lives in a crooked house version of this in his "Ghost Zone", which may or may not also be the Phantom Zone or Limbo.
Literature
In Lawrence Watt-EvansThe Legends Of Ethshar novels, there are magical tapestries used for transportation — you weave a picture of where you want to be. One highly advanced magician makes a tapestry of a "in a void of nothingness" castle and thereby brings into being a little pied-a-terre (pied-a-void?) for himself and his mistress... but when the return route gets blocked, said mistress ends up trapped in said castle for a few centuries.
In the works of H. P. Lovecraft, the Daemon Sultan Azathoth is said to sit on his black throne in the center of the universe (or possibly the multiverse), surrounded by the Ultimate Void.
Tabletop Games
The tomb-bodies of the Neverborn in Exalted are both Ominous Floating Mountain-Thingies and one of the setting's (many) groups of Big Bads. They really want to fall into the Void and finish dying, and they're willing to destroy all of Creation to get there.
Several in Planescape, most notably the Doomguard citadels which float on the borders between the Negative Energy Plane and the Quasielemental Planes; and Orcus's crumbling fortress of Tcian Sumere also in the Negative. These all likely inspired the Fortress of Regrets in Planescape: Torment (below).
Videogames
Castle Bleck and Smithy's Factory in the Mario RPGs. The former is basically a floating, glowing castle in monochrome colours set in the middle of a void that is actually called "The Void" (which Count Bleck created for his Suicidal Cosmic Temper Tantrum), and the latter is a series of platforming elements floating in a dark blue void of nothingness.
While also a prison, the Oubliette from Metroid Prime: Hunters, although it gets pulled back to normal space so that you can fight the Final Boss inside it.
The (spectacular) Chaos capital in Warhammer Online, the Inevitable City, is located on the edge of a vast crater beneath a seething hole in reality. The Eternal Citadel, the fortress where the Big Bad lurks, sits on one of many floating chunks of rock hanging beneath the Alien Sky.
In Kingdom Hearts II we have the villain's hideout, the Castle That Never Was, which is literally 'right next to the Realm of Nothingness.'
In Dragon Age the Black City, which supposedly was the home of The Maker and the location of heaven before it was corrupted by the hubris of mortals, appears as a vaguely city shaped blob of darkness in the otherwise empty sky of TheFade. Interestingly enough, the Black City is the only permanent landmark in the Fade.
You fight one of these as a boss in Dragon Quest VI. On foot!
Perimeter has the Frames - ominous floating cities housing what is left of Mankind.
The preserve of many Sci Fi or Speculative Fiction series, these are Exactly What It Says on the Tin: Floating bases somewhere in their own solar system or galaxy with nothing for miles. Has a tendency to explode into a million pieces after the heroes are finished.
Azathoth. He resides in the center of the universe.
Live-Action TV
The Cylon Colony was floating in empty space during "The Plan", but by the time of "Daybreak" it had been moved to the accretion disk of a black hole so that it would be hard for anyone but a Cylon to 1) find it and 2) be able to enter it. Extra points for being a black techno-organic construct◊ with eight arms, each one miles long.
Tabletop Games
The Zurich Station from Shadowrun, located on Earth's orbit. It houses the central governing body of all Evil Mega Corps. THE. MOST. SECURE. FACILITY. EVAR.
"The Rock", the Fortress Monastery of the Dark Angels chapter of Space Marines in Warhammer 40,000. It is all that remains of their homeworld of Caliban, a literal castle on a jut of rock floating in space. It has since been sealed against the void and equipped with engines to travel the stars, moving from world to world to find new recruits. Unlike a lot of other examples though, this also qualifies as Dark Is Not Evil. Well, mostly...
Freeport 7 in Freelancer counts to some degree: It explodes in a million pieces at the very beginning of the game, and it looks like the only base in the entire system (there's an unofficial mod that lets you enter the Freeport 7 system, which is indeed completely empty except for the remains of Freeport 7).
The Floating Fortress in the NES and MSX2 versions of Final Fantasy I. In remakes, though, it's a castle floating in the clouds. Except the castle itself is not evil; it was constructed by the Lefeinish before Tiamat the Wind Fiend screwed them over and seized the castle.
The Air Castle in Phantasy Star IV. Explained in better detail below.
And then there are these, often found on Floating Continents. They're just floating buildings found a few hundred (or thousand) miles high in the sky. Have a tendency to come to earth with an enormous crash once the evil inhabitant is defeated.
Schneizel's Damocles◊ fortress from Code Geass may count as this. It's basically an amalgamation of the earlier airships with a Britannian-style palace, using float systems and energy shields introduced earlier in the series. knowing Schneizel, who had those technologies commissioned, this was all a part of the plan. True to its name, it's not only shaped like a hovering sword, but also houses a stockpile of FLEIJA warheads that could be launched on any city at Schneizel's whim, thus enforcing peace.
Episode 6 of SoulTaker was aptly named "The Malevolent Stratosphere Castle" for its location. It was a safe haven for a mutant who had become jaded with his work for the Hospital and sought to end his life in peace.
Rather viciously subverted in ElfQuest, which begins (almost) with a magical fairytale castle appearing in midair... above a group of terrified neanderthals, who promptly attack its elfin occupants when it comes crashing to the ground moments later.
Fan Works
The Immortal Game: The boon that Nihilus asks for in exchange for serving Titan is a floating fortress, something her Co DragonEsteem views as tacky and cliche. And true to form, it collapses when Nihilus is defeated by the Elements of Harmony.
Fairy Tales
The giant's castle in Jack And The Beanstalk. In some versions, it is implied that there's a whole world of giants up in the clouds.
Films — Animated
Duck Tales The Movie Treasure Of The Lost Lamp has a great example when the evil sorceror Merlock uses the Genie's magic to turn Scrooge's money bin into a Floating Castle that is very ominous. It's not floating by design though; Merlock specifically wished to "return home in his new home". Scrooge just defeats him before they get to the destination.
Literature
The floating castle made of clouds from Piers Anthony's Xanth series counts as it is currently the home of the Demon Xanth, his consort Chlorine and their son. Somewhat subverted in that the Demon currently in residence isn't actually evil.
Isaac Asimov wrote a short story entitled Shah Guido G. which features the titular despot ruling future Earth from his flying city before it is destroyed by piling on too much weight. (The title, when pronounced correctly, warns the reader that the entire story is a set-up for a truly hideous pun.)
Castle Black in Steven Brust's Dragaera, a non-evil example. Of course, the Empire is littered with the ruins of castles that fell out of the sky the last time The Magic Went Away.
The Castle in the Air from Norman Juster's The Phantom Tollbooth. (Actually a floating prison, inhabited by a couple of captive princesses.)
The original Laputa appears in Jonathan Swift's Gulliver's Travels, where it is a floating island inhabited by scholars. Their relationship with the peasants who live below is often strained, but they are not out-and-out evil.
In the The Legends Of Ethshar series, the same wizard mentioned under void of nothingness also created a flying castle in the skies, which was brought down by a Fantastic Nuke.
Silver towers of Tzeentch in Warhammer 40000 are floating ominous floating towers powered by daemonic energy. They don't float all that high, tho, only a few meters above ground, but they're still Ominous Floating Towers that shoot bolts of sorcerous energy at people.
Mobile floating castles were used in the War of the Lance, from the Dragonlance D&D setting. They were built by the bad guys, so qualify as ominous too.
Flattery Wyvernspur's castle, Temple in the Sky and several cases when the top half of a wizard's tower remained in a good condition and in its proper place for several centuries after lower floors were completely (and violently) removed. Starting with the one from which young Elminster, then Elmara, with her band of adventurers were kicked out in The Making of a Mage.
Exalted has the (now ruined) Flying Fortress of Bagrash Köl, as well as the Titan fortresses. Which can quite cheerfully wipe a city off the map.
Floating fortresses in Swashbucklers of the Seven Skies, where everything is either on a Floating Continent or free-floating in the Skies. Of particular note was the Astramorte, an obvious Expy of the Death Star, destroyed in a daring raid taking advantage of seemingly inconsequential vulnerabilities.
The nation of Breland in Eberron has a pair of mobile, floating fortresses that are something of a subversion, as they are more like land-based aircraft carriers. They only float a short distance above the ground and move very slowly and were not as useful in the Last War as Breland had hoped, but were still powerful symbols of Breland's magical and military might. (Breland is one of the few unambiguously Good nations, as well, meaning the fortresses are not even particularly ominous.)
Videogames
Not exactly owned by the villain, but the Advance Base Rakion at the Mesos Floor in Ace Online/Air Rivals can look rather intimidating to inexperienced pilots. It doesn't help that it's the largest map in the entire game and that players from ANI and BCU must fight for control of the Advance Base to put it into use.
The Moonflower Palace of Dark Cloud 2 used to be one, until it engaged the heroes' own flying fortress, Paznos, and it was sent hurtling right towards Palm Brinks. Paznos' robot mode was barely able to ground it elsewhere.
Giga Wing 's fourth stage is set on a Floating Continent, and the stage following it one-ups it with a floating city.
In The Legend of Dragoon, most of the ancient Wingly cities were like this until the Dragon Campaign.
The Black Omen in Chrono Trigger floats in the air for thousands of years, such that when it appears, people comment on it regardless of the time period you visit. In fact, it's been around so long that people aren't even scared of it anymore, even though is a obsidian floating Magi Tech imposing thing that's even named the Black Omen.
Sky Dragon's Isle takes to the skies and transforms into Terra Tower, aka Dinopolis, in Chrono Cross.
Tiamat's Floating Tower in Final Fantasy, mentioned in Dissidia and it's sequel with the dungeon 'Dreams of a Flying Castle' and mentioned in the Cosmos Reports.
The Castle of Emperor Palamecia in Final Fantasy II. It's kept aloft by a massively destructive Cyclone, and can only be reached with the help of a flying dragon.
Ultimecia's castle in Final Fantasy VIII. It's so floaty that it has to be held down with improbably huge chains.
The Mana Fortress in Secret Of Mana, which once destroyed the world.
Sky Fortress Bahamut from Final Fantasy XII. Double bonus since it's also an Evil Tower of Ominousness, tall enough to reach the clouds with its upper decks while its bottom floats just a few hundred feet above ground level.
And yet another example in Yoshis Island DS, which has to be reached by space rocket (although it's shown in the clouds in the intro), and like most Mario examples, crashes to the ground after the Final Boss is defeated.
Also from the Tales series, Tales Of Vesperia has the Ancient Tower of Tarqaron.
Valen's Fortress in Threads Of Fate manifests itself as a floating, pointy fortress.
The end cutscene of Viewtiful Joe 2 shows one of these, allegedly the source of the Black V-Watch and Black Film. However...
The Scourge Necropoli in Warcraft, most notably Naxxramas in World of Warcraft (an Instance that was revamped for Wrath of the Lich King), and Acherus The Ebon Hold (The Death Knight's equivalent to Moonglade). They also showed up all over the place during the Zombie Apocalypse event before the release of Wrath of the Lich King.
Tempest Keep and its satellite structures in The Burning Crusade float over the edge of Outland, above a drop into the Twisting Nether.
Necron Monoliths in Dawn Of War: Dark Crusade. The only Necron building that can produce units, once fully upgraded it flies, teleports decent distances, and brings enormous firepower to bear on anything unfortunate enough to get in its path. If it ends up being severely damaged, it teleports back to its original location. Not really ominous, as that implies that your doom is merely impending, Monoliths are the final seal on your tomb.
While not so much ominous or a boss level, Wario Land Shake It! has Airytale Castle, Prism Prison and possibly Launchpad Labryinth in this kind of floating building.
In the The Legend of Zelda: Ocarina of Time, Ganondorf does this to his eventual hideout of Hyrule Castle. Annoyingly, the void is only about 50 feet from the nearest cliff edge and you spend the latter two-thirds of the game only that far away from the final boss.
In The Legend of Zelda: Majora's Mask, the whole plot and lots of other things revolve around the moon. The moon has a hideous face on it and Majora's mask is trying to crush the land with it. It also is the final dungeon and where you fight the Mask at the end.
Both Legend of Legaia and its sequel do this, although the first one does score extra points for having the tower being a piece of junk made to fly specifically to invoke this trope and lure the player's to a Load-Bearing Boss fight.
Power Stone 2 takes place in a castle in the sky. In addition to collecting the titular wish-granting MacGuffins, the objective of the game is for the player characters to fight their way out of the castle. True to the form of this trope, defeating Dr. Erode, the master of the castle, in the Final Battle leads to the destruction of the castle.
Malefor has this as his lair in the final The Legend of Spyro game. Between the second and third game, Malefor retook the Dragon Temple after being set free, then used his magic to lift it high about the ground and use it as his castle. For added ominousness, it's over a volcano.
This is a somewhat popular model of base to build in Minecraft. Due to gravity not working on most blocks, it can be made out of dirt, stone, brick, wood, metal or even, theoretically, water and ice.
In Billy Hatcher And The Giant Egg, Giant Palace initially comes off across this way in its first mission. It's subverted though when Billy and his chums boot DarkRaven out, bringing morning. As a result Giant Palace becomes a much nicer place.
Killorn Keep in Ultima Underworld II, suspended above a desert, serves as an outpost to the Big Bad and a Mirror Universe to Britannia. Due to the technical limitations of the game you can't see outside it, so you have to take the developer's word for it. It's kept afloat by two brain creatures, and if you kill them it comes crashing to the ground.
This trope is probably what the Magus from Gargoyles had in mind, when he froze them in their stone form "until the castle rises above the clouds". The possibility that buildings would one day be tall enough for the place to become a clouddeck penthouse didn't occur to him.
