Ominous Pipe Organ

Anime and Manga

 * Naruto:
 * Orochimaru's theme 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 Maniacal Shrieking = Hidan's Theme.
 * Ominous Chanting times 2 plus Ominous Pipe Organ = Pain's and Madara's theme.

Films — Animated

 * The Duke of Owls in Rock-A-Doodle played an organ for his Villain Song.