I'm not counting Henchmen Villains like Bob the Goon or Bane from Batman & Robin, mobsters like Carmine Falcone or Sal Maroni or corrupt business men like Max Shrek or John Dagett. I also decided not to count Talia Al Ghul because while she might have technically counted as the main villain of The Dark Knight Rises she was only revealed at the end and wasn't around long enough to be established as a complex villain. Also I tend to change my mind a lot so this list is not 100% official.
1. The Joker (The Dark Knight)
2. The Joker (Batman)
3. Bane (The Dark Knight Rises)
4. Two-Face (The Dark Knight)
5. Catwoman (Batman Returns)
6. Ra's Al Ghul (Batman Begins)
7. Catwoman (The Dark Knight Rises)
8. The Scarecrow (Batman Begins)
9. The Penguin (Batman Returns)
10. The Riddler (Batman Forever)
11. Two-Face (Batman Forever)
12. Poison Ivy (Batman & Robin)
13. Mr Freeze (Batman & Robin)