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1027 Lex Luthor of the Justice Lords universe, JL
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1032 Hades, JL
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1082 Mad Hatter, Batman Bad Blood
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1097 The Boss, Superman (1942 cartoon, Showdown)
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1112 Anycard, Teen Titans
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1113 Tony Zucco, The Batman
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1123 Black Spider, Young Justice
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1126 Killer Frost, JL Unlimited
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1128 Red Hood, Batman Under the Red Hood
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1150 Wizard, Young Justice
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1176 Dwarfstar, Brave and Bold
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1175 Uthool (possessing Batman), JL Action
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1193 Tiger Shark, Brave and Bold
Offline
A couple answers I'm deeming close enough: Imperium is close enough to Imperium Leader. The other case is one of those situations I'll give you due to my lack of familiarity with the source material. For B&B Tigress, the B&B Wiki says that Artemis Crock (the character pictured) was being groomed by her mother (the previous Tigress) to be the next Tigress, which the DC Wiki says she did use the alias. Since I haven't watched, I'll allow that. Beyond that, everyone correct; list updated.
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1048 Starburst, Static Shock
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1278 Mad Hatter, Young Justice
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1159 Ra's Al Ghul, BTAS
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1171 Deadshot, Brave and Bold
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1239 Catwoman, Return of the Caped Crusaders
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1316 Minotaur, Super Friends
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1301 Jax-Ur, Superman TAS
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1310 Nostromos, BTAS
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1280 The 50s Joker from Legends of the Dark Knight episode of BTAS
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1282 Count Vertigo, BTAS
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1283 Brand, Brave and Bold
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1288 Bleez, GL
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1289 Professor Chang, Teen Titans
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1286 Livewire, JL Gods and Monsters
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1274 Lex Luthor, JL Dark Apokalips War
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1261 Black Manta, Young Justice