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A fair share of these are seen inFist of the North Star, such as the Cassandra prison tower and the Imperial Capital.
The Tokyo Metropolitan Government Building in Digimon Tamers. Any scene the building is shown, ominous music plays. One character even remarks he's gets a creepy feeling from it, despite the structure being a well-known landmark. It becomes even creepier when its assimilated by the D-Reaper after the latter invades the real world, eventually creating the Mother Reaper out of it.
The Post-Crisis version of Lex Luthor held bragging rights to the tallest skyscraper in the world, even beating out the Petronas Towers of Kuala Lumpur. The original towers were a riff on Manhattan's World Trade Center, except with the towers shaped like Luthor's initials. This was later retconned into a giant claw-like monstrosity hanging over the city.
Various incarnations of the LexCorp/LuthorCorp building appear in Superman: The Animated Series, Lois and Clark (in which Lex commits suicide from jumping from it) and Smallville, of which the exteriors shots were of the Government of Canada building in Vancouver, which is right next to the Marine Building which serves as the Daily Planet.
Lex: I must confess that I love the fact that everyone in the city has to look up in order to see me. (Lois & Clark, "Pilot")
In many fairy tales, the villainess put the heroine in a tower and gets herself in and out by climbing the heroine's hair. "Rapunzel" is the most familiar of these, but there are many others, such as "Snow-White-Fire-Red". These are always the work of the villainess, and the heroine is always eager to escape.
Burning Black: There are eight Dark Spires dotting Dimmsdale's skyline that all work together to nullify fairies and their magic, a Master Spire and its seven Support Spires. They're to be upgraded later to National Spires, and it's this upgrade that Timmy and his friends are trying to prevent.
Queen Of Shadows: The Shadowkhan fortress has at least one of these, which contains the Queen's personal living quarters.
Star Wars: The second Death Star had a tower at its north pole, containing the Emperor's penthouse suite, complete with handy-dandy bottomless pit that led into the reactor core for some reason. The first Death Star had a similar tower in it, according to The Force Unleashed.
The aptly, and affectionately nicknamed "Wizards Tower", the prominent observation platform aboard the Confederate flagship Invisible Hand in Revenge of the Sith. It's clearly meant to be very evocative of the Death Star spire too.
Tomorrow Never Dies: Elliot Carver's building in Saigon, which dwarfs everything else and has a giant poster of his face on the side.
Inspector Gadget: The gothic-looking skyscaper which houses Sanford Scolex's corporate headquarters. Although it looks like something created for a movie baddie, it is actually a real building, the PPG Place in Pittsburgh.
The Anton Furst-designed Gotham City in 1989's Batman was a city full of these. Carl Grissom's penthouse suite definitely qualifies, though.
55 Central Park West becomes one of these in Ghostbusters, thanks to its fictional backstory of being designed by Mad Architect Ivo Shandor.
In The Shop On Main Street, a film shot in Nazi-allied, fascist Slovakia in 1942, a wooden tower is being built in the central square. It turns out to be a monument to the fascist Hlinka Guard militia, and it is dedicated in a chilling ceremony.
With the way Lord Business acts, it would be highly uncharacteristic for him not to have this. It's a soaring, infinitely-floored Octan office tower complete with thunder and lightning in The LEGO Movie. Also includes a Think Tank to imprison and torture Master Builders in.
Dol Guldur in Mirkwood. As it happens, Minas Morgul (originally Minas Ithil), Cirith Ungol, and Orthanc were originally Nice Towers of Niceness before being repossessed; having been built by good guys in the form of the exiled Númenóreans. Minas Anor/Tirith in Gondor was one of the few such towers that was spared from being abandoned or taken over by evil... and of course, there was an older Minas Tirith in the First Age that Sauron did take over.
The Towers of Teeth at the Black Gate.
The original Big Bad's base in The Silmarillion (Utumno), however, was a classic Elaborate Underground Base. Except that it seems to have been approximately the size of the entire country of Gondor. It was so freaking huge that even rubbish heaps it produced passed for outer walls and Evil Towers Of Ominousness of their own right.
Morgoth's second base, the triune mountains of Thangorodrim.
The MGM Grand Hotel in Las Vegas becomes a straight one for Randall Flagg in The Stand.
The White Tower in Robert Jordan's The Wheel of Time books, especially after Elaida's Face-Heel Turn. Mazrim Taim builds and rules the Black Tower, but this is actually a village; the name was chosen specifically as a reference to the other one. Taim does build a palace that he rules from that counts though. And that's not including the Tower of Ghenji, which is probably a portal to a dimension with Alien Geometry. Or the Towers of Midnight, which were the place where the a'dam, a collar to enslave magic users were made. Or, for that matter, the tower that Moridin has recently started using in the Blight. While the 13th book probably won't show the (for the series) literal Towers of Midnight (they're several thousand miles away), it's probably not called Tower of Midnight for no reason. There's a lot of ominousness to go around.
Jessica Meats' Codename Omega stories have Grey's Tower. It's not much of a skyscraper but it is in the middle of York and there were planning permission issues - they weren't allowed a helipad. The fact that Mrs Grey was able to build it at all implies evil influence.
Warhammer 40,000: Dark Apostle had the construction of one of these by the Word Bearers as the main part of the story, it went into vivid detail of it being built using the enslaved populace of the world as both labor and mortar for the slabs of stone. The foul corruption of the tower eventually made the work force grow to love the tower and some jumped to their deaths in the pit surrounding it to become closer to it, dragging any who were on the chain line with them but not under the tower's sway with them.
Prince Xizor in Star Wars: Shadows of the Empire has one, of the skyscraper variety. Partially subverted in that every building on Coruscant is a skyscraper. It collapses after Lando Calrissian drops a thermal detonator in the garbage chute.
The Shadow King in The City of Dreaming Books has a tower. Located in a huge vault in the deepest reaching of the city-spanning catacombs.
The Ministry of Truth in 1984 is an "enormous, pyramidal structure of white concrete, soaring up terrace after terrace, three hundred metres into the air." Not a wholly inaccurate exaggeration of Stalinesque architectural ambitions. But somehow an eerily prescient description of the real-life Ryugyong Hotel in Pyongyang from 1992 to 2008.
Harrenhal from A Song of Ice and Fire was originally built by a man named Harren as a fortress/monument to himself. It consisted of five towers, said to be among the tallest in Westeros. Then Aegon the Conqueror showed up with his three dragons and melted much of it, turning it instantly from some Jerk Ass's self-congratulatory monument to a cursed White Elephant of a fortress that brings bad luck to whoever makes it their seat of power. The "curse" actually has a fairly mundane in-universe explanation: the size of Harrenhal makes it an sought after by rivals for the prestige of holding it, yet is so big it is hard to effectively defend. No wonder it keeps changing hands and bringing ill fortune to those who try and hold it.
The only person who prospered after sacking Harrenhal thus far has been Roose Bolton, who's such a Magnificent Bastard he's apparently even capable of subverting curses.
The Targaryen fortress of Dragonstone is the most exotic castle in the realm, located on an island in the middle of nowhere. Many don't see the wisdom of shaping its towers to look like dragons.
Memory, Sorrow, and Thorn subverts this by having the Final Battle take place atop Green Angel Tower, a place of inhuman beauty and the sole above-ground remnant of the ancient Sithi city of Asu'a (humans built the Hayholt atop the old city after capturing it). It's also not coincidentally the location of the Storm King's attempted Heroic Sacrifice five hundred years ago, and the place he chooses to reenter the world in the present. It's still a big-ass tower where the heroes fight the Big Bad, though.
Most of the conflict in Otherland occurs within the titular network, but a significant portion of the climax takes place in the real-world skyscraper that forms the headquarters of J Corp. Black, ominous, and massively taller than anything else nearby, it's a suitable home for Corrupt Corporate Executive Felix Jongleur and gets spectacularly flattened when the Other decides to commit suicide via Death from Above.
In Bronding's Honour, there's the Bright Tower which can apparently only be seen as far as the Bronding's Hold, making a lot of other clans believe the Brondings are seeing things. It's ominous, but is said to be a 'good' place.
The Emberverse's Castle Todenangst, built by Genre Savvy tyrant Norman Arminger, is a deliberate attempt to evoke this effect.
Patricia C. Wrede's Caught In Crystal has the Twisted Tower, a black, bent tower inhabited by a shadowy evil creature. Our heroine was part of the first disastrous expedition to the Tower, and now must return, sixteen years later, to discover what really happened the first time and finally set it right.
Belgariad. Cthol Mishrak. Don't forget the iron castle/tower on WHEELS Torak had PULLED to the Battle of Vo Mimbre.
The Riftwar Cycle has the Sorcerer's Isle, which holds an ominous castle that has a cold blue light shining from its tower's windows and sends sheets of silver light into the sky overhead. A subversion in that it's designed to be maximally ominous to scare people away, but all the lights and sounds don't mean anything. It's even largely left empty; the entire point of the tower is ominousness so the sorcerer in residence can be left alone.
Ridjeck Thome (aka Foul's Crèche) from the Chronicles of Thomas Covenant is a combination Evil Tower of Ominousness and Elaborate Underground Base in the tradition of Angband; though it features a truly ominous tower, the bulk of the structure, including Lord Foul's throne room, is below ground.
Live Action TV
Frasier: Played for laughs and lampshaded when the staff of the radio station have to confront their boss in an office building known as The Black Tower.
Wolfram & Hart's Los Angeles branch corporate building. Angel partially lampshades this: "You set things in motion, play your little games up here in your glass and chrome tower, and people die - innocent people."
Jakanja, the villain group from Ninpuu Sentai Hurricanger plunged their space ship vertically into the earth, resulting in a variation of this trope. The American counterpart Power Rangers Ninja Storm averts this as the villains have a completely different spaceship which stays in orbit of the planet.
The Battersea Power Station becomes the London headquarters of Cybus Industries in "Rise of the Cybermen."
Classic series example: The Tower of the Three Who Rule in the Fourth Doctor story, "State of Decay." This being Doctor Who, the Tower is really a crashed, defunct spaceship.
Also from the classic series, the Tower of Rassilon. When the Doctor spots it he knows he's in the Death Zone, which is unpleasant as its name suggests.
There are a couple in Merlin but the titular Dark Tower takes the cake.
Subverted with the tower where Rapunzel is trapped in the Once Upon a Time version of that story: It seems like it should be this, but is in fact just an old tower of no special significance. Rapunzel is only trapped there by a physical embodiment of her own fear, created when she ate an anxiety-curing vegetable called Nightroot. It would have appeared to stalk her whether she was in the tower or not.
The song "The Dark Tower of Abyss" by Rhapsody is about such a tower.
In the Ptolus setting for Dungeons & Dragons, the city of Ptolus lies in the shadow of the impossibly tall Spire. Though not many people in the city realize it, the entire spire is hollow and holds a vault of evil artifacts, and on top of that is the castle so tainted by its former Big Bad occupant that the gods themselves still keep it locked tight thousands of years after his death.
Halfway up the Spire is the fortress of a Slightly Less Big Bad. He plunged most of a continent into winter for years as a weapon of mass destruction, created monstrous laboratories in which to create monstrous armies, and generally was bad news for everyone and everything. And he measures up to the halfway point of the original big bad.
In the prequel Ys Origin, it takes up the whole game, but features more varied environments like a flooded prison, lava area, and sand-filled area.
Both Baldur's Gate and Baldur's Gate 2 have towers as the Bonus Dungeon of the add-ons. Tales of the Sword Coast has Durlags Tower, a deathtrap dungeon build by a mad dwarf king, while Throne of Bhaal had the Watcher's Keep, which sits atop the prison of a Demonic Overlord of Hell. As a slight subversion, the Watcher's Keep is entered by climbing a massive set of stairs to reach the main door, located at it's top.
God of War II has the Spire of the Fates, which can be seen in the distance for most of game. On closer inspection it turns out to be not just an ordinary tower, though.
Shadow of the Colossus has the Temple that holds the 16 icons, which is a huge tower which can be seen from miles away.
It's so ominous and huge that its top is obscured by clouds, and the next two episodes in the game focus almost entirely on delaying its exploding before so everyone can evacuate, and when it does anyway, cleaning up the mess — and superportal — afterwards.
The Depot at Nova Prospekt may also count. When viewed from outside, it towers over the entire complex. Up close, it has the same kind of prisoner transport system as the Citadel's, and is literally made from the old prison's materials, thanks to the giant crushing walls nearby.
The final level of Mass Effect 1 has Shepard climbing the Citadel tower which has been seized by Saren's Geth. This is notable in that Shepard does not ascend the tower the way it's meant to be done, but instead by exiting it and walking up the side. The boss fight with Saren takes place at the top in the council chamber.
Thane's recruitment mission in Mass Effect 2 involves fighting your way to the top of a pair of towers connected by a skybridge. Though since you take high-speed elevators most of the way you only actually fight on about five floors.
Mirage Tower in the original Final Fantasy I, a spiral-shaped structure whose very top contains a teleporter into the Sky Warriors' Floating Castle.
The Emperor's Tower within the Cyclone in Final Fantasy II. Castle Palamecia and Pandaemonium also qualify.
The Crystal Tower at the center of the Ancients' Maze, in Final Fantasy III, where Xande awaits. It stretches upwards far, far above the clouds (it takes both of the Nintendo DS' screens to show just part of it) and holds the altar/teleporter to the Dark World at the top.
There are two of these in Final Fantasy IV — the Tower of Zot, where Golbez makes his lair, and the Tower of Bab-il, which extends into the center of the planet and has immense powers, triggered by the game's Plot Coupons.
Fork Tower, Phoenix Tower, and the four Barrier Towers that maintain the shield around Exdeath's castle in Final Fantasy V. Fortunately, the party only needs to visit one; Fork Tower and Phoenix Tower are also optional. Walz Tower, where the Water Crystal resides until shortly into the game, sinks into the ocean and becomes an underwater dungeon for the party to traverse from top to bottom, but it's not exactly "evil" per se.
Kefka has one in Final Fantasy VI. TWO, if you count the Cult of Kefka tower. And then there's the cutscene while flying to the Imperial Palace.
In Final Fantasy VII, Shinra HQ, which rises from ground level and serves as the Midgar Plate's central pillar, certainly has more than enough floors to count (and the player can choose to climb up the stairs). President Shinra's office sits on top.
Final Fantasy XI has Delkfutt's Tower, an immense structure made of white bone-like material ("cermet") where one of the major bosses of the Rise of the Zilart storyline resides. Castle Zvahl Keep might also count, especially since it leads to the Throne Room of the Shadow Lord, the game's first Big Bad.
Final Fantasy XII's massive Pharos Lighthouse. Based on the real Pharos Lighthouse, except much, much bigger, and filled with vicious monsters. There's also Sky Fortress Bahamut, which has the appearance of a floating tower but you only get to travel in a small part of it. It eventually crashes just outside of Rabanastre and becomes a tower by default.
Ganon's Tower from A Link to the Past, Ocarina of Time, and The Wind Waker. The latter is in Old Hyrule, not far from Hyrule Castle, but since the whole area is inside an underwater dome, it's not visible from anywhere else. A Link to the Past also has the Tower area of Hyrule Castle, after it's usurped by Agahnim.
The Clock Tower serves as the gateway between Link's home dimension and the world explored in the game, the ominous clock ticking off the time until the moon crashes, a representation of which appears on the screen throughout the game, the point where you reappear each time you rewind to the first day, the arena for both the first and the penultimate battle against the Skull Kid wearing Majora's Mask, and the point from which you travel to the moon for the final dungeon and final battle.
The Stone Tower Temple in Ikana Canyon. Notable because part of the dungeon is going back outside and hitting a switch to invert the entire place.
The Tower of Spirits from Spirit Tracks. The only times you can't see it from your train are when there's physical objects (mountains, trees and the like) blocking your view.
Overlord has one of these — the game being what it is, it's your character's home base. However by Overlord II it has been destroyed when the Tower Heart powering it was tampered with, exploding and corrupting the lands of the first game with a magical plague. You still have sort of an Evil Tower as a base, though it's now located in the Netherworld and hangs upside-down like a giant evil stalactite.
Area X-2 from Mega Man Zero 3, which extends all the way into space.
The Tower of Salvation in Tales of Symphonia subverts this in two different ways; its artful ivory countenance is rather un-ominous and serves as a symbol of hope for both worlds, even after you discover that the creators are evil, and the tower itself isn't a lair — it just contains a teleporter to one.
The Tower of Tarqaron in Tales of Vesperia on the other hand plays it completely straight. A huge, flying, black city topped with a giant tower housing a Magitek weapon powered by the Life Energy of every human in the world.
The Castle Keep in nearly every Castlevania game, where Dracula is fought (there are several towers in the games, including the infamous Clock Tower where Death is usually fought, but the Castle Keep is always the tallest one).
In Castlevania: Lords of Shadow the final battle takes place on the Lord of the Dead's Tower (Its a giant pillar that is larger even then the others, and is flanked by two massive lion statues.
Geese Tower in Fatal Fury, the tallest building in Southtown, and the location of Geese's demise in every continuity.
In Golden Sun, there are four elemental lighthouses whose beacons can be lit with gems called the Elemental Stars. Lighting these beacons is the objective of the villains of both the first and second games, and every time you enter one of the lighthouses you'll have to fight a boss battle at the top. They're not really supervillain lairs, per se, but supervillains do tend to congregate there.
Bowser's Castle from the Super Mario Bros.. series, as well as every castle for every other villain in the series as well. The Shroob Castle in Mario & Luigi: Partners in Time is this kind of sinister place with a huge statue of Princess Shroob, Castle Bleck is a huge castle/tower situated in the void and there's probably a lot of other examples.
The Tower of Valni is taken over by monsters early on in Fire Emblem: The Sacred Stones. More and more floors are unlocked for you to clear as the plot progresses.
Chrono Trigger: Who can forget the scene where the party first sees Magus's Lair in all its gloomy glory?
Chrono Cross: It's only the most chilling part of either Chrono series where the party first enters the Dead Sea and sees the creepy-as-hell Tower of Geddon looming on the frozen waves.
Earlier in the game, Fort Dragonia, site of very dramatic events that change the protagonist's life forever.
Also, Terra Tower, built by the descendants of the Reptites in an alternate future.
Space Quest IV had the Xenon Super Computer dome in the Space Quest XII time period, which now served as Vohaul's base of operations. It looks like a "vast boil" on the ruined landscape.
Dr. Loboto's tower lab in Psychonauts, as well as the thorny tower in the Brain Tumbler Experiment.
An Evil Tower of Ominousness shows up as the Very Definitely Final Dungeon in Medal of Honor Airborne, of all places in the form of the Flak Tower, a giant concrete tower the size of a large town. Zero Punctuation remarks that "I was unaware the Nazis had a gigantic armored concrete tower that could only be described as a DOOM FORTRESS". Although the Flak Tower is a real WWII German war structure, the allies never actually attacked one during the war (and the Soviets could only siege them until the people inside ran out of food).
The first Breath of Fire game has many wonderful towers to climb, from beginning to end.
Dungeons in Daggerfall have random outsides but most of them involve a mound with inlaid stairs (going down, supposedly). However, it also includes full and ruined castle-like backdrops, some in what appear to be former cities or towns, or cut into giant trees. Rarely are their names correctly descriptive. All of the main quest dungeon exteriors are unique (Orsinium is the most unique one), save for the first and the last dungeons of the main quest. In fact, a plainclothes entrance to the Mantellan Crux is accessible on a very small island off of the main map, northwest from your ship.
The Lich King's Frozen Throne is located on top of a tall spire of ice. Karazhan, the tower of Medivh, is a more straight example, being an ominous tower with evil things inside, including ominous pipe organ music.
The Frozen Throne isn't just on top of a tall spire of ice, it IS the tall spire of ice. Another example would be Icecrown Citadel, a massive tower built around the Frozen Throne. It's a giant evil tower built around a giant evil tower.
But the original and still the best is Blackrock Spire, a black dragon doom fortress made out of a Blackrock/Black Tooth Grin orc doom fortress made out of a Dark Iron Dwarf doom fortress originally intended to carry out the commands of a chaotic demigod made of lava. And it still houses all of them!.
And then there's also the tower of Auchindoun, though it may not count because it only became evil after it blew up. Also, it is more of an evil ring of remaining tall support beams for a dome or amphitheater of evil.
The Mana Forges in Netherstorm are massive structures that drain magic from the space around them, but the big daddy of all these is Tempest Keep which MOVES.
Taken Up to Eleven in Catacylsm which boasts both the Twilight Citadel and the Sulfuron Spire, made of twisted metal and on fire respectively. The latter of which is the little brother of the MASSIVE spire that houses the Elemental Embodiment of aforesaid fire.
The Tattered Spire from Fable II, which, when completed, can be seen from any beach in Albion.
Syrup Castle in the Wario Land series. An absolutely huge skull shaped castle on a mountain, it's probably big enough to hold a small town, and in both games it appears in has the entire last world inside it. So much in fact the first level inside the area in the second game is actually called 'Get to the Castle' and has an ominous opening cut scene showing Wario looking up at the building.
Even in Pokemon Red And Blue, on the monochrome Game Boy, Pokémon Tower in Lavender Town pulls this off very well, given it's a towering cemetery that happens to have some bad guys at the top. Which leads to one question: Since it's a tower... where are the dead buried? It appears in Gold/Silver/Crystal as well, but as a normal tower.
Realgam Tower in Pokémon Colosseum, since it's controlled by the villains. The sequel gets rid of the "evil" and "ominousness" parts and just makes it a normal tower, similar to the above entry.
GhostWidow's base is a tall tower in the first area (it's also a Clown Car Base). Several zones in the game have a skyscraper draped in Arachnos banners that acts as a base for them.
Lord Recluse's Broadcast Tower in Grandville is the biggest and most ominous of the towers on Primal Earth. It's big, red, spidery, and is designed to steal the powers of every Hero on Earth. In Praetoria, the honor goes to Emperor Cole's Watchtower in Nova Praetoria, which is supposedly visible throughout the city. It's not so much an Evil Tower of Ominousness as a Shiny Tower of Gray and Gray Morality, but it fits the bill.
Fort Drakon. Technically it's simply part of the city of Denerim, but effectively turns into an evil tower once the Darkspawn invade the city at the end of the game, which also turns the sky red and gives the tower an even eviler look. It also serves as the final dungeon after one of the Archdemon's wings is damaged and must land atop the tower.
The Circle Of Magi's tower also looks like one (complete with a large full moon in the background), and like Fort Drakon, basically turns into an evil tower after a demon invasion from within. It gets better after you beat the mission, but still looks just as ominous as ever.
Reconstructed with Fallout 3s Dunwich Building, a foreboding tower in an already Used Future, especially in contrast to the uncommonly bright and shiny Tenpenny Tower nearby. The entire site is an homage to H.P. Lovecraft.
The Tower of Babel in Doom, final location of the second episode. Actual tower properties are not apparent when you get there, though, as all you do once you get there is fight the Cyberdemon at the base of it, with the player character not climbing it until the end-episode text once said demon is killed.
Lost In Shadow starts with a boy's shadow being cut from his body and being tossed of a giant tower. That tower isn't this trope, the Dark Tower is.
Devil May Cry 3 has Temen-ni-Gru, a tower in which most of the game takes place.
The Watcher's Tower in El Shaddai: Ascension of the Metatron, which makes up the bulk of the game. As it was created by fallen angels, the interior is so mind mindbogglingly large, it's not so much divided into individual floors, as into individual worlds.
Shining Soul features a massive evil tower called, creatively, "Dark Tower". Filled with harpies and robots; the remnants of of civilization long since past.
Rokakku builds one in Shibuya Terminal in Jet Set Radio Future. It's a freaky piece of modern art, and contained in a warped space inside is the final battle zone. It has no name canonically, but due to one of Rokakku's lines when he's talking it up some fans have taken to calling it "Irrelevant".
The Citadel in Beyond Divinity. Actually, it's not the final dungeon but very first one.
Might and Magic VII features a downplayed example in William Setag's Tower. It's not actually that tall (any ominousness comes mostly from the fact that there are very few towers period in Deyja), and except for one specific optional quest all you do with it is talk with William Setag, self-proclaimed Villain — but it is definitely a tower that looks out of place and is controlled by evil (Setag does things like kidnap 'the fairest lady in Erathia' just for the sake of doing it).
In Robopon, Dr. Disc's tower is this in the first game. There's no door for you to enter the tower, except at the very top. Your solution? Blow it up. Zero Castle is this too, though with the warp pads, you don't have to climb all the way up.
Clive Barker's Undying: One of the manor's towers has an unearthly purple halo stretching into the sky, marking the portal to Oneiros.
"Shounen Kininden Tsumuji": has a huge tower called the Shadow Tower which leads to the floating Demon Castle in the sky.
Meio's Tower in Strider is the Big Bad's main residence and the symbol of his absolute rule, and is so high that is disappears among the clouds.
In Radio Active Panda, students from a rival ominous tower of mad scientist-type evil (from the OTHER mad scientist tower/academy of mad robotics who has a moon base) pull a prank by stockpiling garden gnomes all the way to the on the 42th floor. The pile of gnomes is a third ominous tower in its own right - considering the pile is probably telescope-visible from earth as a red spot and the largest known nuke wouldn't remove them all.
The Templar Towers in TwoKinds actually turned out to be giant magic batteries which have the nasty side effect of slowly turning the brains of Bastins and Keidrans into mush, making their lands ripe for a Templar invasion.
Count Disdain's castle in Van Von Hunter. Van, unable to find Count Disdain's lair, asks a local for help. The local asks if he's "tried the ominous fortress on the mountaintop."
The Black Rose Tower in Tasakeru is a complex case, not so much evil, but definitely ominous. Originally built by a would-be world conqueror, it was quickly abandoned when said conqueror did a Heel-Face Turn. It was revealed later to have strange magical properties, including repairing itself when damaged and limited shapeshifting. The inside is even weirder: it adapts to the needs of whomever calls it their home.
From Gargoyles; the Erie Building is the world's tallest, located in Manhattan. It's the home and office of villain David Xanatos, and just to crank up the ominous factor, it's topped with a real Scottish castle from the 10th century. Plus live gargoyles, at the beginning and end of the series.
On Kim Possible, Dr Drakken's Caribbean lair, the only one he uses more than once, is a tower, on a mountain, on an island, that's supposedly haunted.
In Disney's Sleeping Beauty, one of the scariest straight examples was the setting of the final confrontation. Also a rare female villain-version.
On Phineasand Ferb, Doofenschmirtz Evil Incorporated is headquartered in a big purple skyscraper.
In My Little Pony: Friendship Is Magic, KingSombra magically converted the central castle of the Crystal Empire into this during his rule a millenium ago. It turns back to normal in his absence, though it still contains several dark magic traps that remain active. He also used it as the hiding place of the Crystal Heart, because he knew his subjects were so terrified of the place that none of them would ever dare enter, no matter how desperate their situation became.
In Transformers Prime, the Decepticons created a their own evil tower on Earth called Darkmount.
Tom Terrific's foe Isotope Feeney resides in an ivory tower.
In the Total Drama All Stars episode "You Regatta be Kidding Me" Mike discovers one in his own mind setting up a Story Arc, considering with him meeting and freeing his other personalities along the way.