Villain Song/Fan Works

In the Bleach fandom, Humble Shopkeeper has one of the characters declaring she wants a villain song to "underline [her] bad-ass-ery". It involves the line "I'll paint the moon red with his blood", a chorus of wolves and evil laughter. Since it takes place in a realistic setting, it's pretty much as weird as it sounds.
"Kira", a Death Note Filk Song to the tune of Michael Jackson's "Thriller".
Portal 2's Wheatley gets one to the tune of Oogie Boogie's Villain Song, as shown here.
- Miracle of Sound gave Wheatley an orignal song entitled Wheatley's Song
The Adventures of Irving and Friends gives up the self aware "This is the villain song".
Despite Touhou containing reams of fantastic music, none of them are songs, and calling any of the enemies villains is not quite accurate; however, that hasn't stopped the fandom from giving some of the antagonists their own Villain Songs based on their respective leitmotifs. Among others, Remilia's swells with charisma, Yukari's is appropriately sinister, and Yuyuko's is a tragic dirge on the mysteries of death.
It's only written lyrics for now, but BEN gets a fan-made Major-General Song Villain Song here, detailing his victory over Jadusable's sanity and promising the same fate for everyone following the story.
Cyros from The Legend Of Spyro: A New Dawn gets "Into The Great Unknown", which she uses to scare her brother Pyrus into aiding her Evil Plan. Later on, she gets "Let Your Secrets Out", where she uses her powers to cause Cynder and Ember's hidden feelings to come to the surface. She also gets a short spell later on that transfers Empress Tyrania's energy into a jewel she can use. Justified in that she is an egotistical music lover and a Evil Diva who uses songs to cast spells.
- Cyros gets one more during the Finale called "Welcome To Your Final Show", which is pretty much a straight up Villain Song about how she intends to kill her brother and Ember, all the while using her Musical Assassin powers to try and do so. She was Drunk on the Dark Side at the time, so naturally she's more hammy than usual.
Decks Fall Everyone Dies plays this straight and sort of subverts it. Duke gets a villain song in which he gloats about how he reigns over everyone using dice games and sexiness, but in the very same song, he hints at a nagging sense of guilt over it.
In the Pony POV Series, Princess Gaia, Fluttershy's Super-Powered Evil Side and the second Big Bad gets two. The first is a ponyified version of "Come Little Children" from Hocus Pocus and the second is a Dark Reprise of Fluttershy's "So Many Wonders" song, telling how her world is safe and perfect and no one will ever have to leave it... And will forget their old lives entirely. It also serves a purpose, as she's an Evil Diva who can trap ponies through song.
- Discord has gotten several. His father, Havoc got one called "Here's To Chaos" as well.
Several fan songs have been written for Discord.
- And here's one for the Diamond Dogs!
Tumblr user Megan Phntm Grl has recorded a villain song for Loki circa The Avengers entitled "Bow to Me". It is, appropriately enough, based on "Der Letzte Tanz" from Elisabeth (listed below in the Theatre section).
Getting Back on Your Hooves has one for Checker Monarch called "Through My Eyes", an "I Am" Song detailing her worldview and manipulative mindset. It's also a Dark Reprise of Trixie's earlier song "Through New Eyes", fitting, as they're actually sisters.
A few songs have popped up in Calvin at Camp episodes, notably the movie parodies. To name some...
- "Destroy All That's in My Path," a parody of "Poor Unfortunate Souls," sung by the Volleyball of Terror.
- "Darkling," a parody of "Gaston," sung by the ghosts from Ghost Master.
- "Why Me/Double D Reprise," a parody of "Why Me" and "Prince Ali Reprise," sung by Bowser.
- "You'll Never Beat This Boss," a parody of "You're Only Second Rate," also sung by Bowser.
- "Go After Other Guys," a parody of "Kidnap the Sandy Claws," sung by the Kankers.