Not all pinball machines have an antagonist, but I think it ads a lot to the games that do. I think of an antagonist first of all as a character, not just an object like a black hole or the ocean. This character works against you, the player, and sometimes even revels in your failure.
Some antagonists taunt the player like Yagov on F-14, The Sorcerer on Sorcerer, and The Pharaoh. Some have re-appeared in sequels like The Black Knight, The T-rex in Data East and Stern's JP, and the Martians in Attack and Revenge. The earliest antagonist I can think of is 1972's Fireball, but I'm sure there were earlier ones I'm not familiar with.
My top three are:
1. Sparky - MET
2. The Genie - TOTAN
3. Rudy - Funhouse
So, What are your top 3 pinball antagonists?