Ominous Pipe Organ



For some reason, organ music and villainy seem to go hand in hand. Perhaps it just sounds sinister and scary. But, in any case, if a character has organ music for his Leitmotif, it's a sure sign he isn't going to be petting any dogs.

Combine this with Ominous Latin Chanting and/or some For Doom the Bell Tolls, and he's got Big Bad written all over him.

Sometimes this analogy goes so far to show the villain sitting at a big spooky pipe organ, playing ominous tunes, as the heroes walk in on him. This iconic scene was probably inspired by The Phantom Of The Opera, whose villain is often similarly shown with his sinister organ. The standard music for this scene is the Toccata and Fugue In D Minor by Johann Sebastian Bach. Bonus points, however, if they are playing their own Leitmotif. Even better if it contains lots of diminished seventh chords.

The exception to the organs = villainy rule is if you're in a church, but the existence of the Corrupt Church and God Is Evil help to blur that distinction. If the organ is accompanying a good religion, then the music is generally more subdued and ethereal rather than overtly "ominous".

Anime and Manga

 * Kagato in Tenchi Muyo is, well, not quite introduced, but featured, playing a series-original Bach-esque piece on a truly enormous science-fictional organ.
 * Orochimaru's theme in Naruto is the Toccata and Fugue in D Minor on a pipe organ, with some Asian flute and shamisen thrown in for good measure.
 * Ominous Chanting+ Ominous Pipe Organ + Creepy Manical Shrieking= Hidan's Theme.
 * Ominous Chanting times 2 plus Ominous Pipe Organ = Pain's theme
 * rape at the hands of Big Bad Apos in Mnemosyne combines this with Ominous Latin Chanting, and takes it all the way up to What Do You Mean Its Not Symbolic when it's committed at a Buddhist Temple, with her chained and nailed to a stone lamp post, no less.
 * Played straight during the first appearance of Isaak Fernand von K&Atilde;&curren;mpfer in Trinity Blood: when Abel finds him, he plays Sagrada Familia's pipe organ which he equipped with the Silent Noise system that.
 * Lady Debonair from the second season of Magic Knight Rayearth.
 * In Magical Girl Lyrical Nanoha StrikerS, the Numbers attack to the theme of a pipe organ. And the Hard Light Magical Computer of their coordinator Uno has a keyboard that looks like organ keys.
 * In the tenth Pokémon movie, Darkrai's Leitmotif contains organs and bells, befitting a Dark-type Pokemon that can literally cause nightmares.
 * In the first Pokémon movie (only the original Japanese version since the score was rewritten for the English speaking audiences) Mewtwo's theme is played on the organ. Lots of diminished chords and chromaticism; following the cliches to the letter. The opening leitmotif is D-E-F-C# (Dm -> Cdim7).
 * The theme for Nakazato's GT-R in Initial D is Toccata and Fugue.
 * Akechi Mitsuhide from Sengoku Basara gets an Ominous Pipe Organ for his anime Leitmotif.
 * In Shugo Chara, the intro to Hoshina Utau's theme song (by Nana Mizuki no less) "Meikyuu Butterfly" is this. The song itself is actually plot relevant.
 * In Chrono Crusade, Joshua Christopher is a boy with holy powers who's been kidnapped by the Big Bad. Guess what instrument he plays to channel his powers?
 * In Princess Tutu, one of Drosselmeyer's leitmotifs is the Nutcracker March played in minor key on a pipe organ to an unsettling effect.
 * Xanxus from Katekyo Hitman Reborn tends to have Ominous Pipe Organ music in the background whenever he turns up.
 * Kiddy Grade: the last third of the series contains two closely-linked tunes, both with ominous pipe organs, that represent the main "antagonist" of the last arc.
 * In Sailor Moon, Eudial challenges Haruka and Michiru to a showdown at the Marine Cathedral. When they arrive, she's playing the Bach Toccata and Fugue on the organ to help them find her.
 * Which turns out to be a recording on a tape.
 * Slayers Next has a guitar tune used for exposition sequences. When it's not just "everyday" exposition but Lina learning that the Lord of Nightmares, the source of her strongest spell,  we get the same tune, but upgraded to this trope.
 * In the Second Season of Space Battleship Yamato (a.k.a. "Star Blazers"), the theme of the antagonist White Comet Empire is a dark and imposing Pipe Organ track - as if the sound the comet produces while moving (the screeching of many souls crying out in terror) wasn't enough to clue you in.
 * The Read or Die OVA features an evil reincarnation of Ludwig Van Beethoven playing a massive pipe organ on a rocket.
 * The Professor Layton and The Eternal Diva animated film tops the previous example by having a pipe organ that is also a giant clockwork orchestra, a, and a . When the true Big Bad is revealed, he gets the Ominous Pipe Organ as background music.
 * Rozen Maiden has this as well. "Broken World" fits this trope to a T, plenty of destruction foretold.
 * Revolutionary Girl Utena uses the organ at certain ominous moments. Or just as elevator music for the Student Council for extra drama.
 * Nasu Veronica plays the organ in Saint Seiya the Lost Canvas. While manipulating the corpses of children.
 * The Demon Sisters' theme from Panty and Stocking With Garterbelt combines this with (of course) stripper music, no doubt to emphasize their Lawful Evil (and infernal) natures.

Comic Books

 * One of Yoko Tsuno's adventures involves an instrument called the Devil's Organ, whose sound can drive listeners to insanity or death.

Film

 * Signor Forte from Disney's Beauty and The Beast The Enchanted Christmas IS an Ominous Pipe Organ.
 * Davy Jones in Pirates of the Caribbean. The only reason he's able to do it is that his ship is alive. He plays it with his beard.
 * Which is probably inspired by Captain Nemo in 20,000 Leagues Under The Sea.
 * More Disney: Both the ride and film version of The Haunted Mansion have a big giant organ. The Disneyland version's organ comes from ''20,000 Leagues Under The Sea", and in the film, someone plays that famous Bach piece on the mansion's organ.
 * Sir August De Wynter in The Avengers 1998.
 * Professor Fate in the movie The Great Race.
 * Former Chief Inspector Dreyfus in The Pink Panther Strikes Again played a version of "Tiptoe Through the Tulips" instead of the usual Bach Toccata.
 * Subverted in The Ghost and Mr. Chicken, as the villain turns out to be.
 * In The Abominable Dr. Phibes, Dr. Phibes plays Felix Mendelssohn's "War March of the Priests". On a jazz organ.
 * Averted in a Sorry I Left the BGM On moment in Wallace and Gromit: Curse of the Were-Rabbit.
 * Max, from Sunset Boulevard, plays the pipe organ rather ominously (if not very well) in the background in several scenes. This is commented on by Joe.
 * "Pruit Igoe and Prophecies" during Dr. Manhattan's backstory in Watchmen.
 * And on that note, the original songs from Philip Glass's soundtrack to the film Koyaanisqatsi.
 * The Duke of Owls in Rock a Doodle played an organ for his Villain Song.
 * In Gremlins 2, one of the gremlins is shown playing Tocatta and Fugue on an organ, complete with Phantom-style mask.
 * In Beneath the Planet of the Apes, the mutants sing hymns praising their god - a nuclear missile with a cobalt bomb warhead.
 * Not a pipe organ, but has the same principle: Return to Oz features an Ominous Mandolin played by "Princess Mombi".
 * In Barbarella Durand-Durand tortures the title character by playing an organ-like device called the Excessive Machine with her in it.
 * This has to be subverted or played with or something, because it kills people by orgasming them to death. And Barbarella overloads it.
 * The opening theme of Sweeney Todd: The Demon Barber of Fleet Street.
 * The iTunes exclusive track "Outlands part II" for Tron Legacy uses an Ominous Electric Organ.
 * "Hellfire" from The Hunchback of Notre Dame.
 * The original Carnival of Souls is full of ominous pipe organ music.

Literature

 * Professor Aronnax walks in on Captain Nemo playing the pipe organ in his study, but subverts this trope in that he's actually weeping.
 * He also plays the organ in a somewhat unusual manner, using only the black keys (what today would be the white keys).
 * Parodied in the Discworld novel Carpe Jugulum, in which a traditionally-minded vampire has an organ ... but it's one of Bloody Stupid Johnson's Clock Punk synthesizers, with a wide variety of screams, wolf-howls and similar Hammer Horror sound effects.
 * Lawrence from Cryptonomicon began playing his local church's organ because the previous performer was kicked for being "too dramatic".

Live Action TV

 * Doctor Who, "Pyramids of Mars": Ibrahim Namin, a sinister worshiper of Sutekh (ancient Egyptian devil-like figure) plays the organ.
 * Sutekh summons him by telekinetically playing the organ, and when Sutekh sends his Dragon to take command, Namin apparently activates the time corridor by playing the organ, thus giving the impression that Osiran technology is powered by organ music.
 * In "The Seeds of Doom" Chase plays an atonal electronic instrument instead, but that's mainly for his plants' benefit.
 * Countdown With Keith Olbermann uses a pipe organ playing Toccata and Fugue for its "Worst Person in the World" segment.
 * Toccata and Fugue is played in Boardwalk Empire after Richard Harrow does his first assassination, which is kind of a visual joke in that Harrow looks a lot like the (post-Lon Chaney) Phantom of the Opera. Then, there's sort of a Diegetic Switch and the music is shown to be playing at a silent movie elsewhere.

Music

 * If the opening of Vangelis Papathanassiou's Nucleogenesis 1 (from the Albedo 0.39 album) hasn't been used for this purpose, it should.
 * Siena by Turmion Katilot has a example of this at a couple of parts in this song.
 * Unquestioned maestro of organ composers J. S. Bach both played this trope straight and averted it. The aforementioned Toccata and Fugue BWV 565 (probably an arrangement of a solo violin piece) certainly has a dark and evil feel to it, but Sebastian's other organ music (including organ parts to go with some of the cantatas) shows the entire array of characters possible in music.
 * The organ solo at the climax of the third movement of Ralph Vaughan Williams' "Sinfonia antartica".
 * Nox Arcana prominently features a pipe organ in many of their songs. Melancholia and The Masque Of Red Death have arguably the most ominous tunes.
 * Used in several Type O Negative songs, notably "Haunted".
 * Muse's song Megalomania uses one of these. It's pretty darn ominous.
 * The beginning of Rob Zombie's "Return of the Phantom Stranger".
 * Iron Butterfly's "In-A-Gadda-Da-Vida".
 * In Limp Bizkit's "Counterfeit", an electric keyboard imitating an organ provides an ominous mood and feel.
 * Jan Zwart's "Toccata on Psalm 146". Ominous Dutch Chanting optional.
 * Vernian. Process. These guys love them some Ominous Pipe Organ music. Lead singer Joshua Pfeiffer even lampshaded it at the end of a show, introducing the band then declaring "...and we like Goth music, if you can't tell!" during the one minute, eight second organ outro to their song "Vagues de Vapeur."
 * The Clotho section and the start of the Atropos section from Emerson Lake and Palmer's "The Three Fates".
 * "Jane Seymour" from Rick Wakeman's The Six Wives Of Henry VIII.

Tabletop Games

 * Advanced Dungeons and Dragons
 * Module I6 Ravenloft has an illusion of Count Strahd von Zarovich playing an organ in his castle.
 * Module RA1 Feast of Goblyns had a dopppleganger playing a pipe organ during an evil religious service.
 * Organ music is the theme of the Adepta Sororitas in Warhammer 40000: Dawn of War, which is quite appropriate. Since Adepta Sororitas field a pipe organ mounted on a tank. That shoots missile barrages. Fired by a Sister on top of the tank with a keyboard. Playing Imperial hymns.
 * Probably also an allusion to "Stalin's Organ" (that's how German soldiers nicknamed the first Soviet multiple rocket launch system).
 * Knights of the Dinner Table #168 "Bait & Tackle" section (adventure seeds). In "The Pipe Organ", a vampire plays a pipe organ to lure PCs to their doom.
 * In the Call of Cthulhu adventure The Dreaming Stone, the Dracula-like servant of Nyarlathotep plays a harpsichord in his mansion on the moon that cause some sanity loss.

Theater

 * Entry score of Sweeney Todd: The Demon Barber of Fleet Street.
 * As mentioned, the trendsetter would be the opening overture of The Phantom of the Opera, as well as (of course) the phantom's Villain Song.
 * Elisabeth uses this trope with aplomb in the Act I number "Alle Fragen sind gestellt", which also counts as Mood Whiplash from the tender love song that preceded it and Soundtrack Dissonance (a compelled-sounding choral piece predicting the singers' eventual doom at the heroine's wedding).

Theme Parks

 * Disney Theme Parks: Aside from the above mentioned The Haunted Mansion, Journey Into Imagination used to feature Dreamfinder playing one in the Tales of Terror sequence.

Video Games

 * World of Warcraft The Burning Crusade: The Opera area in Karazhan.
 * Ganondorf from The Legend of Zelda Ocarina of Time is one of the more famous examples; as Link moves up the tower in the center of Ganon's Castle, the Ominous Pipe Organ music (which happens to be a redone and extended version of the Leitmotif of the building's owner) gets louder and louder, until he reaches the top -- and finds Ganondorf playing it.
 * And then there's Blizzeta's theme in Twilight Princess.
 * Ghirahim's leitmotif in The Legend of Zelda Skyward Sword mixes in a pipe organ. Rather than one of the big booming ones, however, it's a smaller, more playful one, which serves to emphasize Ghirahim's similar Psychopathic Manchild demeanor.
 * One of the bosses in Castle Crashers alternates between fighting you and playing a pipe organ in a church. He cant be hurt while at the organ and as he plays the organ launches bombs in increasingly complex patterns.
 * While he's a general-purpose user of this, Neclord's appearance in Suikoden II is probably the crown of this trope. Entering a fog-shrouded, ruined castle on the lake's edge, surrounded by a graveyard containing the restless corpses of the castle-town's slaughtered inhabitants... ominous organ-music playing as you fight your way past undead ghouls and minor vampires, finding your way through the crumbling labyrinth of the castle's hallways, finally making your way to the top of the tallest tower, to find Neclord sitting with his back to you, playing the organ - and as he turns to face you, the music stops in mid-chord. Chilling.
 * In Suikoden I, he plays the popular Wedding March as a funeral dirge (appropriate considering what happens to his brides), and in both games his Leifmotif (Called "We Love Our Master") uses the Organ.
 * The heroes of Chrono Trigger have to play a few chords on an organ to uncover the hidden passageway in a (monster-run) church. Lavos's theme is a classic example of ominous organ music.
 * In the sequel/gaiden Radical Dreamers, a pipe organ song plays when you descend to Lynx's hiding place.
 * The final showdown with Bowser in Super Mario 64 is accompanied by an ominous solo organ piece. Hear for yourself.
 * Bowser themes in general have Ominous Pipe Organ.
 * The generic dungeon theme in Super Mario RPG is also played on a pipe organ, with a few grace piano notes thrown in.
 * The final battle against Smithy's first form in Super Mario RPG has this along with industrial mechanical sounds.
 * The Castle theme from New Super Mario Bros.
 * Damon Gant's theme in Phoenix Wright Ace Attorney. He even has an enormous pipe organ in his office...the chief of police's office. It also seems to be modeled after the very one on this page image. Phoenix comments on what a massive waste of taxpayer money this is. According to Gumshoe, Gant goes so far as to use the organ for Cool and Unusual Punishment (he sits misbehaving cops in his office and plays it for several hours; the unfortunate victim is left deaf for a week).
 * So he shows them his huge organ?
 * Also, Richard Wellington's cellphone has the quitessential organ tune, Toccata et Fugue, as its ringtone. In the same case, it's used for major effect during the Phoenix Wright's nightmare and when.
 * The Rival of Ace Attorney Investigations 2, Hakari Mikagami, has one as the centerpiece of her theme. It's used to reinforce her "holy" appearance.
 * Used heavily in Chapter 9 of Drakengard, especially during the scene in which
 * Yggdrassil in Tales of Symphonia, including all the music when you fight him. His androgynous and angelic appearance and status as head of a Path of Inspiration only underscores the sinister.
 * Tales of Phantasia has this as background music when you enter the cathedral that leads to Fenrir's cave.
 * Possibly lampshaded in Tales of the Abyss - The first time you fight
 * Considering how music in general is one of the major themes of TOTA (Prophecies are called 'Scores' or 'the Score', the resident Crystal Dragon Jesus is the personification of sound, various church titles and ranks include Melodist, Maestro, Conductor, Cantor, etc.) and in fact is the key to using much of Auldrant's Applied Phlebotinum, this is perhaps more justified than many of the other examples on this page.
 * The Lord of Jewels in Legend of Mana has this as its battle music.
 * The dungeon music is replaced by Ominous Pipe Organ music between the penultimate and final bosses in Lunar: Silver Star Story (that's the remake, by the way.) It's truly great music to monologue over, as the Magic Emperor demonstrates.
 * The semi-operatic pipe organ piece "Dancing Mad", Kefka's Final Boss music in Final Fantasy VI. Only slightly less famous than its Ominous Latin Chanting successor in the next game. Of course, considering the fact that the game's intro music and the music that plays on the world map before obtaining the Falcon also use an Ominous Pipe Organ, it's not surprising that the final boss music contains even more Ominous Pipe Organ. (Incidentally, all three examples overlap with For Doom the Bell Tolls.)
 * "Dancing Mad" also shamelessly rips off Toccata and Fugue in D Minor in many parts, especially during the organ solo in the third movement.
 * Ultimecia from Final Fantasy VIII greets her visitors with "The Castle"
 * Kuja in Final Fantasy IX also gets "Immoral Rhythm" and "Dark Messenger".
 * His boss, Garland, has "The Keeper of Time."
 * And the original Final Fantasy organ themist has to be Golbez in Final Fantasy IV. His theme even shamelessly steals riffs from "Toccata & Fugue in D-Minor". The Nintendo DS remake has this lampshaded in the sound test by having Edward, who comments on the tracks, referring to the pipe organ as the hallmark of Golbez's theme.
 * Also, Chaos, the Big Bad of Final Fantasy I, features the Ominous Pipe Organ in his fight music. (Remakes only, the original has no boss music.)
 * Also done to full effect in Final Fantasy X-2 since it's how the Big Bad commands the Weapon of Mass Destruction.
 * An organ is also used for the ominous, frantic theme "Vegnagun Starting".
 * Also Galdes final theme.
 * Kingdom Hearts has it's own Organ-driven theme (well, it sounds organ-ish) in the form of Forze Del Male, which plays during the battle with Rikunort in Hollow Bastion.
 * "Graceful Assassin" combines Ominous Pipe Organ and For Doom the Bell Tolls into quite a dramatic tune against the (first) final boss of the game.
 * Ramirez's theme in Skies of Arcadia begins putting on the Ominous Pipe Organ near the end -- as if the ringing doom bell, the chaotic drum track, the sinister violin backdrop and the piano clinks weren't disturbing enough. It's a good clue-in to the fact that
 * The later Castlevania games are all about Ominous Pipe Organ music, especially the opening of Super Castlevania IV.
 * One of the late-game bosses in the Nintendo DS Rhythm Game Ontamarama uses pipe organs as part of his theme music.
 * As does Gregorio in the Playstation 2 Rhythm Game Gitaroo Man.
 * Ultima VII uses fairly light and pleasant organ music as the theme for The Fellowship.
 * Elyon's battle theme in Breath of Fire Dragon Quarter. It might even
 * Earlier in the series, the dungeon music from the grand church of "St. Eva" in Breath of Fire II
 * Big Bad Tabuu in Super Smash Bros Brawl doesn't have the pipe all the way through, but one segment of his theme has it. Rather noticable because it contrasts the rest.
 * The remixes of the Zelda Overworld/Underworld music and Luigis Mansion theme incorporate this as well.
 * The music for the final battle in the first Front Mission game, Destructive Logic, is nothing but ominous pipe organ music.
 * Not to be outdone, Gun Hazard (from the same franchise) gives us the equally chilling Nature.
 * As well as the track used for the last stretch of the game, Atlas.
 * The battle with the Magician in The House of the Dead 2 is preceded with pipe organ music before cutting to his own boss battle music.
 * That's The Jimmy Hart Version of "Toccata & Fugue in D Minor".
 * What's interesting is that the song actually goes on for a whole lot longer than what's played in-game.
 * The opening theme used in 1 and 2 is more or less the track equivilent of a four-man band: starting off with the organ, it's soon joined by sombar bell tolling, an ominous bass a capella choir, and squares things off with some good old brass-and-drum Orchestral Bombing.
 * Megaman Legends. Organ music = Final Boss, in both games.
 * As it happens, the organ music in the first game is another Bach piece, called "Little" Fugue in G Minor. The first part of the battle has a faithful rendition, but they use a somewhat more epic remix for round two.
 * Brady Culture in Sam and Max: Culture Shock. He's not a very ominous villain, though.
 * Serguei Borodine in Syberia. This is a variation of the trope because Serguei himself cannot play the organ but builds a robot who has the ability to play it.
 * At the end of the Musical Town stage in the SNES Sparkster, the title character encounters Axel Gear playing a pipe organ before they fight.
 * The Grand Cathedral theme from Serious Sam: The Second Encounter has something like this combined with For Doom the Bell Tolls as its central component.
 * Eternal Darkness uses an organ to open a secret compartment. This sequence will be important later.
 * An eerie, if not completely ominous pipe organ can be heard in church interiors in The Matrix Online
 * Ys I and II: The 12th floor of Darm Tower features an ominous organ tune called "Devil's Wind" that drains Adol's HP and prevents him from progressing until he smashes one of the pillars on the outer gallery.
 * The Perfect Run Final Boss battle in Ray Crisis. Aptly titled "Root of all evil"
 * The Final Boss battle in Silent Hill 3. Although it's not on the official soundtrack.
 * It is, however, on the movie soundtrack, titled Samael.
 * The chapel music in The Seventh Guest. A different ominous organ tune is played during the "sacrifice" cutscene in the same room. Also, Dutton's Leitmotif.
 * Devil May Cry likes using organs in it's music. Listen to this, this, or this.
 * Devil Sunday, the opening theme of the game (extended into a sinister fugue when you enter the cathedral).
 * The Final Boss thene of Live a Live begins with a pipe organ, and the Bad Ending consists of nothing but a pipe organ (eventually adding For Doom the Bell Tolls and just one big, ongoing explosion).
 * The Disgaea series is rather fond of pipe organs, what with its demonic bent. Disgaea 3's "Fugue of Hell", Mao's Leitmotif, is particularly noticeable in this regard.
 * Perfect Cherry Blossom, the seventh game in the Touhou series, has a very interesting example. Youmu's theme combines an organ with hard rock, and is very fast paced while still being ominous. But the thing is, not only is the character in question The Dragon rather than the Big Bad, but she's not evil in any sense of the word, even by Touhou standards. The third stage in the same game also has Ominous Pipe Organ music, which the creator himself has pointed out sounds like a Disc One Final Dungeon.
 * On the other hand, vampire Remilia Scarlet, from the same series, plays this straight - in the fighting spinoff Scarlet Weather Rhapsody, her already epic, piano-driven theme song Septette for the Dead Princess gets rearranged into a masterpiece that makes liberal use of organs, violins, piano, drums and electric guitar. Most notable is the kickass organ intro at the beginning, which follows the melody throughout the song and serves to drive the point home that you're fighting against a five hundred year old devil.
 * The Shin Megami Tensei series in nearly all of its incarnations has made liberal use of pipe organ music, the most universally consistent being the music played during the Dark Cathedral fusion room. SMT 3: Nocturne takes this trope to an especial extreme.
 * In the Heaven's Feel route of Fate Stay Night, the BGM for much of the final battle (against ) is "All the Evils of the World", a very ominous remix of the (itself rather spooky) "Little Church on the Hill" which acts as the theme song for, who is.
 * Beatrice's theme from Umineko no Naku Koro Ni involves an Ominous Pipe Organ. It also has a tendency to start up in the middle of other themes as she teleports into the scene out of nowhere, so it can happen unexpectedly.
 * Rose Crimson~ Sasori No Harawata.
 * The Organists from Brutal Legend are little more than a ghostly pipe organ on wheels.
 * The final boss of Pikmin has this in his background music. Not quite as ominous as many of the other examples, but way more ominous than any other music in the game.
 * Descole's theme in Professor Layton and The Last Specter.
 * Mother 3 had an organ play when you were in a shrine. That alone wasn't mysterious, until you take your time and if you listen through the whole song, they do a Dark Reprise of the "There's a Railway in Our Village!?" theme, which the real song plays later in the game after
 * Duke Hermeyen of The Last Remnant has an organ-heavy Leitmotif. It's scary.
 * Part of the Boss Rush in Stella Deus the Gate of Eternity takes place on top of a giant ominous organ which also happens to be the control panel for a massive device that's intended to bring about The End of the World As We Know It.
 * False King Allant of Demon's Souls has one during his boss fight.
 * Siter Skain is absolutly in love with this trope with their games full of masterful organ tracks. It would be easier to list those that does not contain any organ.
 * The first boss theme of Refle X Crazy Goddes Virgo, the sixth boss Imperial Gaurd - Scutum - and the Climax Boss theme Raiwat Virgo -Type R- are good examples.
 * Resonance of Fate plays organ music accompanied by an evil choir while you storm the Basilica.
 * Blaz Blue have some organ tracks obviosly mixed with metal but some can hardly be called ominous such as the upbeat The Road to Hope while on the other hand Howling Moon and White Requiem are slightly straighter.
 * And then there is Death Smiles with it's regular boss theme and the final boss theme Hell's Emperor.
 * In King's Quest V Absence Makes the Heart Go Yonder, Mordack's castle has a grotesque pipe organ that can play itself.
 * And in King's Quest VI Heir Today Gone Tomorrow, the ominous pipe organ music plays a grotesque version of Lohengrin and Mendelssohn's Bridal Chorus ! Give it a listen here!
 * Also, the same ominous pipe organ music plays during the first half of "Stopping the Wedding".
 * The Data East game The Great Ragtime Show (AKA Boogie Wings) has a visible pipe organ on which a villain is playing Bach's Toccata and Fugue in D minor.
 * In Resident Evil 4, Salazar's battle music uses this alongside Ominous Chanting.

Web Animation

 * Parodied in The Demented Cartoon Movie, where Evil Blah gets sick of the Ominous Pipe Organ that punctuates his evil rants, and eventually shoots the organist.

Webcomics

 * In Girl Genius, Agatha literally controlled her clanks by playing her theme tune on the silverodeon she spent the prior arc repairing. Agatha IS the heroine, but she's pretty distressed at this point.
 * In Stick Man Stick Man comics, strip 438 and 439 shows Freecell playing on an organ.

Western Animation
"Dot: Well, somebody had to do it."
 * In the Kim Possible episodes "Bad Boy" and "Stop Team Go", Ron Stoppable is turned into his Super Powered Evil Side. While he's fighting, the Toccata and Fugue in D Minor plays as his theme music.
 * The Scooby Doo Show episode "The Harum Scarum Sanitarium". The music accompanies the ghost of a mad doctor.
 * In the Sushi Pack episode "But is it Art?" the control panel for the villain's device that brings paintings to life is a pipe organ (that can rise from the floor, even).
 * Heard (and illustrated) in the intro of Count Duckula.
 * One of these is played by Mr. Ten in Jimmy Two-Shoes.
 * Played for Laughs in Freakazoid. The episode opens with recuring villain Armando Gutierez playing an organ witht he stereotypical opening... followed by a variation of pop goes the weasle
 * Parodied in Animaniacs during their take on "The Three Billy Goats Gruff". Every time someone mentioned the [gasp] troll, there would be a sudden cut to Wakko playing ominous music on the organ. (Except when Wakko said it; then Dot covered for him.)


 * In an episode of SpongeBob SquarePants Patrick encounters Spongebob parodying the infamous Phantom of the Opera scene because he believes the reason everyone is shunning him is because Patrick claims he's ugly (when actually it's just that he has rancid breath and Patrick has no nose to smell this). Made more hilarious by the fact that when confronted Spongebob is wearing gag Groucho Marx glasses.
 * For those of you interested, the episode in question is "Something Smells".