You can do what you want, but I’m steering away from monsters here and instead I’m looking at bad guys (and gals) supernatural or otherwise, who are actively trying to thwart the hero of the movie. I’m also steering away from anti-heroes (which would be another good list).
There are a LOT, so I’m picking 10. In episode order, they are:

• Dr. Krup, aka “The Bat” – 102- THE ROBOT VS. THE AZTEC MUMMY: aka the evil Judge Robert Bork.
• Sidney Chillas – 307- DADDY-O: buttery Bruno VeSota, the poor man’s Sidney Greenstreet, as his evilest.
• Fu Manchu – 323- THE CASTLE OF FU-MANCHU: The dullest villain ever, which makes him more evil.
• Cleolanta – 413- MANHUNT IN SPACE/417- CRASH OF THE MOONS: Opheisha hath no fury like a bitchy suzerain scorned.
• Loukhy, aka Witchiepoo – 422- THE DAY THE EARTH FROZE: Gotta admit she has a bold plan–not many villains have the stones to actually steal the sun.
• Prosser – 501- WARRIOR OF THE LOST WORLD: Gets points for sheer quivering rage; loses points for being a robot.
• Pitch – 521- SANTA CLAUS: hammy and inept though he may be, he’s unforgettable.
• Krankor – 816- PRINCE OF SPACE: The nasal terror from outer space.
• Kalgan – 820- SPACE MUTINY: He’s evil plans largely consist of sitting around in a warehouse basement.
• J.K. Robertson – 821- TIME CHASERS: Everybody’s worst boss; how evil can you get?

Honorable mention
• Troxartas – 703- DEATHSTALKER AND THE WARRIORS FROM HELL: The henpecked villain.