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)
• Lord Farquaad (Shrek)
• King Candy / Turbo (Wreck it Ralph)
• Tai Lung (Kung Fu Panda)
• Pitch (Rise of the Guardians)
• Randel Boggs (Monsters Inc)
• Syndrome (The Incredibles)
• Darla Dimple (Cats Don’t Dance)
• Count Olaf (A series of Unfortunate Events)
• Beetlejuice
• AUTO (WALL-E)
• Cat King (The Cat Returns)

TV Shows

• Zuko (Avatar)
• Azula (Avatar)
• Plankton (SpongeBob)
• Gideon (Gravity Falls)
• Discord (MLP)
• Crowley (Supernatural)
• Sylar (HEROES)
• Ice King (Adventure Time)
• The Lich (Adventure Time)

Video Games

• Bowser (Mario)
• King Dedede (Kirby)
• Marx (Kirby)
• Zero Two (Kirby)
• Master and Crazy Hand (Kirby) (SSB)
• Mr. Dark (Rayman)
• Claus (Mother 3)
• Porky (Mother)
• G-Man (Half-Life)
• Dimitri (Sly Cooper)
• Panda King (Sly Cooper)
• The Contessa (Sly Cooper)
• Don Octavio (Sly Cooper)
• Jean Bison (Sly Cooper)
• Ninetails (Okmai)
• Count Blech (Paper Mario)
• Dimentio (Paper Mario)
• O'Chunks (Paper Mario)
• Mimi (Paper Mario)
• Nastasia (Paper Mario)
• Dooplis (Paper Mario)
• Andrew Ryan (Bioshock)
• Sander Cohen (Bioshock)
• Gilbert Alexander (Bioshock 2)
• The Boss/The Joy (MGS3)
• Revolver Ocelot (MGS)
• Psycho Mantis (MGS1)
• Screaming Mantis (MGS4)
• Laughing Octopus (MGS4)
• Ghadius (Klonoa)
• Maxwell (Don’t Starve)
• Domino Hurley [Love to Hate] (Grim Fandango)
• GLaDOS (portal)
• Lady Yunalesca (FFX)
• Jecht (FFX)
• Grunty (Banjo and Kazooie)
• Woodsman (The Wolf Among Us)
• Eddie Gluskin (Outlast)
• DeRosa (Bravely Default)

Anime

• Team Rocket (pokemon)
• Gregory (GHS)
• Scanty and Kneesocks (Panty and Stocking)
• Lust (FMA)
• Envy (FMA)
• Greed (FMA)
• Gluttony (FMA)
• Pride (FMA)
• Wrath (FMA)