Joker
- The Killing Joke
- The Man Who Laughs
- Lovers and Madmen
- Death in the Family
- The Clown at Midnight
- Arkham Asylum: A Serious House on Serious Earth
- Death of the Family
- The Dark Knight Returns
Harley Quinn
- Mad Love and Other Stories
- No Man’s Land
Riddler
- When Is A Door
- Hush
- King Tut’s Tomb
- Joker’s Asylum vol. 2
- Catwoman: When In Rome
Bane
- Knightfall
- Batman vs. Bane
Killer Croc
- Joker’s Asylum vol. 2
- Arkham Asylum: Madness
Ra’s Al Ghul, Talia Al Ghul
- Son of the Demon
- Bride of the Demon
- Birth of the Demon
- The Chalice
- Death and the Maidens
- Batman and Son (Talia)
- The Resurrection of Ra’s Al Ghul
- Batman Incorporated (Talia)
Poison Ivy
- Hush
- No Man’s Land
- The Long Halloween
Two-Face
- The Long Halloween
- Faces
- The Judas Coin
- Robin: Year One
Clayface
- Monsters
- Detective Comics vol. 3: Emperor Penguin
Hush
- Hush
- Hush Returns
- Heart of Hush
- Streets of Gotham
Scarecrow
- Scarecrow: Year One
- Knightfall
- No Man’s Land
- The Dark Knight vol. 2: Cycle of Violence
The Court of Owls
- The Court of Owls
- The City of Owls
- Night of the Owls
- Gates of Gotham (while the Court does not explicitly appear here, Scott Snyder clearly lays the foundation for their arrival in the New 52 throughout this pre-N52 volume)
Penguin
- Arkham Unhinged
- Detective Comics vol. 3: Emperor Penguin
- Haunted Knight
What about Mr. Freeze?
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I personally don’t have too many comics that feature him, and I don’t like to recommend things without having read them myself. That said, I’ve hard good things about the TPB “Snow” which deals with his origin. If we’re talking non-comic adaptations, there’s the BtAS episode “Heart of Ice,” the animated feature SubZero, Freeze’s appearances in Arkham City and Origins (particularly the “Cold Cold Heart” DLC) and of course, the COOLest of all, “Batman and Robin.” (I kid, I kid…)
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OH! Also, “Gotham Central.”
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