Mr. Freeze-Heart of Ice episode of Batman:TAS. Redefined him to be a tragic figure instead of just a villain with a gimmick
Bane-Knightfall. The way they someone not only strong enough to physically break the bat but also a strategist who planned as well as the Bat. Determined his secret identity and wore him down.
Two-Face-Batman:TAS multiple episodes. Liked that they built up Harvey Dent as character first so you feel bad when he turns. Also he sometimes would do right thing with his perverted sense of justice
Ra’s Al Ghul
Clayface
The Riddler
The riddler, scarecrow, Catwoman
Poison Ivy, Harley Quinn, and Catwoman
Szaz, Hush, pyg, and scarecrow. I know it said 3 but whatever.
And honorable mentions.
Catwoman
Bane
Red hood from Arkham Knight
Riddler
Deadshot and Deathstroke (though Slade is more a Titans villain.)
I think they foil Batman in a equal but unique way from the Joker.
Besides them, I’d have to say Ra’s, but more for Batman vs. The League of Assassins and the Batman/Talia factor
My three other than joker are Two-Face, Ra Al Ghul and Hush
Mr freeze,poison ivy,and penguin
Imma have to say catwoman clayface and and manbat
Scarecrow, riddler, court of the owls
Bane
I’m gonna say Mr. Freeze, Killer Croc, Poison Ivy
And then after that Two Face, Bain, and Penguin
And then Ras, Zizzix, and even though he’s not a Batman villain but they have gone toe to toe, Deathstroke
Catwoman, Bane, and Rasal Goul.
Ras Al Guhl, Riddler, Catwoman
Hush, Bane and Deathstroke.
Penguin, Riddler, Two Face
Mr.freeze, bane, owl man (and joker isnt even in my top 5 favorite bm villains)