I guess this will also include characters who turn good in the end.

Disney Villains

• Hades
• Ursula
• Scar
• Dr. Facilier
• Gaston
• Jafar & Iago
• Maleficent
• Oogie Boogie
• Pete (Goofy Movie)
• Hector Barbossa (Pirates of the Caribbean)
• Davy Jones (Pirates of the Caribbean)

Other Movies

• Audrey II (Little Shop of Horrors)
• Dr. Evil (Austin Powers)
• Eris, Goddess of Discord (Sinbad)
• Fairy Godmother (Shrek 2)

Live Action

• Monk
• Pushing Daisies
• The Good Place
• Breaking Bad
• Parks and Rec
• My Name Is Earl
• Malcolm in the Middle
• Dead Like Me
• Sandman
• Squid Game
• Santa Clarita Diet
• The Umbrella Academy
• The Dark Crystal: Age of Resistance
• Stranger Things
• The Haunting of Hill House

Animated

• Invader Zim
• Ed, Edd, and Eddy
• Courage the Cowardly Dog

Movies/TV

• The Thing
• Ex Machina (thriller)
• Ready or Not
• Perfect Blue
• Candy Man
• Cabin in the Woods
• The Haunting of Hill House
• Silence of the Lambs
• Midnight Mass
• Alien

Games

• SOMA
• Bioshock?
• Dead Space
• Resident Evil
• Silent Hill 2 and 3
• Junji Ito's works
• FNAF
• Mouthwashing

• Paper Mario 1-3
• Mario and Luigi Super Star Saga
• Earthbound/Mother 3
• Legend of Zelda - Windwaker/Twilight/BotW
• Kirby
• Animal Crossing
• Chibi-Robo
• Luigi's Mansion
• Pikmin 1-3
• Ghost Trick
• Banjo Kazooie
• Professor Layton
• Bravely Default
• Phoenix Wright
• Splatoon
• Klonoa
• Rayman
• NiGHTS
• Sonic
• Spyro

• Auron (FFX)
• Captain Haddock (Tintin)
• Peppino (Pizza Tower)
• Vincent Volaju (Cowboy Bebop Movie)

Live Action

• Duplex
• Death Becomes Her
• Little Shop of Horrors
• The Blues Brothers
• The Mask
• Liar Liar
• Cable Guy
• The Truman Show
• A Series of Unfortunate Events
• Fun with Dick and Jane
• The Grinch
• The Muppet Christmas Carol
• Jingle All the Way
• A Christmas Story (1983)
• Spy Kids
• Some Like it Hot
• Bedazzled
• Blast from the Past
• Monkey Bone
• The Mummy