Now this is a great idea for a thread.
Joker: The Killing Joke, Detective Comics 475-476 (the Laughing Fish), 826 (Slayride), Batman 251 (The Joker's Five-Way Revenge), 321 (Dreadful Birthday Dear Joker) 426-429 (Death in the Family), Legends of the Dark Knight 65-68 (Going Sane), Batman: The Man who Laughs.
Two-Face: Eye of the Beholder, Batman/Two-Face Crime and Punishment, Long Shadows, My Own Worst Enemy, A Lonely Place of Dying, Jurisprudence, the Long Halloween, Detective Comics 66-68, 580-581, 755, Batman 234, 313-314, 410-411.
Riddler: Questions Multiply the Mystery, Zero Year, Dark Knight/Dark City, King Tut's Tomb, Paul Dini's Detective Comics, The Riddleless Robberies of the Riddler, Detective Comics 705-707, The Remarkable Ruse of the Riddler, Solitaire.
Penguin: Penguin: Pain and Prejudice, Penguin Triumphant, Batman 548-549 (Penguin Returns), 169 (Partners in Plunder), 586 (Penguin Dreams) Detective Comics 541, 610-611 (Snow and Ice), Joker's Asylum Penguin, Batman Annual 11 (Love Bird), Batman #23.3 (Bullies), The Penguin Affair.
Scarecrow: Mistress of Fear, Fear for Sale, The Six Days of Scarecrow, The Scarecrows Trail of Fear, Fear of Faith, Scarecrow: Master's of Fear, Appearances in Knightfall, Batman 296, 455-457, Nightwing 9-11, Catwoman 58-60.
Poison Ivy: Batman: Poison Ivy, Legends of the Dark Knight 42-43 (Hothouse), Detective Comics 693-694, 751-752, Shadow of the Bat Annual 3, Poison Ivy Cycle of Life and Death, Secret Origins 26, Detective Comics 23.1.
Killer Croc: Requiem for A Killer, Don't mess with Killer Croc, Fast Train to the Wet Dark/Swamp Things, Jokers Asyum: Killer Croc, Under the Skin, Blood in the Water, The Beast Beneath, Crocodile Tears.
Bane: Vengeance of Bane, Knightfall, Bane of the Demon, Batman: Bane, Tabula Rasa/Veritas Liberat, Secret Six, I Am Bane, Bane Conquest.
Ras Al Ghul: The Lazarus Affair, Son of the Demon, Birth of the Demon, Batman Legacy, Tower of Babel, Death and the Maidens, Detective Comics 444-448, 750.
Mad Hatter: Batman Madness, Joker's Asylum: Mad Hatter, Detective Comics 758-760 (Unknowing), All Mimsy were the Borgoroves, The Mad Hatter Goes Straight, The Mad Hatter flips his Lids, Crossed Eyes/Dotty Teas, Robin Year One, All Star Batman 8 (Hats and Bats), Detective Comics 841 (The Wonderland Gang), Gotham Central 19-22 (Unresolved)
Hugo Strange: Legends of the Dark Knight 11-15 (Prey), Detective Comics 471-472 (Strange Apparitions), Gotham Knights 8-11 (Transference), Batman and the Monster Men, Batman Annual #10 (Down to the Bone), Batman 356.
Mr Freeze: Batman: Mr Freeze, Batman 308, Gotham Knights 59, Legends of the Dark Knight 201-203 (Cold Case), Gotham Central 1-2 (In the Line of Duty), All-Star Batman 9 (Ends of the Earth)
Black Mask: War Paint/Faces of Death, The Spidered Face/Web of Scars, Batman Mosiac, Catwoman: Relentless, Batman Under the Hood, Red Hood and the Outlaws Dark Trinity.
Harley Quinn: Batman Harley Quinn, Batman Mad Love, Detective Comics 831, Gotham City Sirens.
Clayface (all versions): Detective Comics 40, 478-479, Batman Annual 11 (Mortal Clay) Mud Pack, Legends of the Dark Knight 89-90 (Clay) Jokers Asylum Clayface, Batman the Dark Knight 23-25, Detective Comics Annual 1 2018 (Clay).
Firefly: Detective Comics 661-662, 689-690, Streets of Gotham 1-2, Batgirl Year One.
Hush: Batman Hush, Heart of Hush, House of Hush.
That went on longer than I thought it would but I just had so many ideas.