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630 Talia, Son of Batman/Bad Blood
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644 Trigon, Teen Titans
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641 Doctor Deemo, Swamp Thing
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514 Cheetah, JL Doom
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611 Mr Mxyzptlk, New Adventures of Superman
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572 Harley Quinn, Suicide Squad Hell to Pay
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565 Deadshot, Gotham Knight
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508 Metallo, Superman/Batman Public Enemies
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Those are correct. List updated. B&B Weather Wizard wound up in this collage series twice, which is annoying, but with that show and the DCAU each having hundreds of villains, probably inevitable.
325B: not from a TV series; not really from comics despite appearances
326: from a TV show, based on comics
328: from a movie, based on comics
335: from a TV show, based on comics
340: from a TV show, based on comics
341: from a movie, based on comics
344: original TV character
345: from a TV show, based on a novel
346: original TV character
347: from a TV show, based on comics
348: original TV character who has since appeared in comics
349: from a TV show, based on comics; comic version non-villainous
350: from a TV show, based on comics
351: from a TV show, based on comics
353: from a TV show, based on comics
354: from a TV show, based on comics
355: original TV character later migrated to the comics
356: from a TV show, based on comics
358: from a movie, based on comics
360: from a movie, based on comics
361: original TV character
363: original TV character
366: from a TV show, based on comics
367: from a TV show, based on comics
368: from a movie, based on comics
371: from a TV show, based on comics
372: from a TV show, based on comics
373: from a TV show, kind of based on comics
374: from a TV show, kind of based on comics
375: from a TV show, based on comics
380: from a TV show, based on comics
381: from a TV show, based on comics
382: from a TV show, based on comics
387: from a TV show, based on comics
388: from a movie, based on comics
390: from a TV show, based on comics
392: original TV character
393: original TV character
394: from a TV show, based on comics
395: original TV character, though a variation of this character has appeared in comics
396: from a movie, based on comics
399: original TV character, though at least one comic character with the same code exist appeared earlier
401: original TV character, but inspired by a comic character
402; from a TV show; looks like the comic version came first but just barely
406: from a movie; based on a non-villainous comic character
407: original TV character
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461 Mr Freeze, BTAS
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521 Mr Freeze, Young Justice
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522 Pre-Flashpoint Captain Cold, Flashpoint Paradox
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536 Captain Cold, Young Justice
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478 Captain Cold, JL New Frontier
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487 Solomon Grundy, Batman Unlimited Monster Mayhem
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540 Clayface (Karlo), Batman Unlimited Monster Mayhem
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523 Starro, Batman Beyond
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541 Icicle Jr, Young Justice
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569 Doctor Blizzard, DCAU
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553 Chronos, JL Action
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499 Poison Ivy, JL Action
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511 Ra's Al Ghul, Batman Under The Red Hood
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502 Bane, Young Justice
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485 Felix Faust, Young Justice
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368 Penguin, Batman Unlimited
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612 Jackson Chappell, Batman Beyond
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388 Bizarro, JL Adventures Trapped in Time
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462 Felix Faust, JL Action
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545 Joker, New Scooby Doo Movies
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Those are all correct. List updated. Annoyingly, Penguin from Batman Unlimited also sneaked in twice.
325B: not from a TV series; not really from comics despite appearances
326: from a TV show, based on comics
328: from a movie, based on comics
335: from a TV show, based on comics
340: from a TV show, based on comics
341: from a movie, based on comics
344: original TV character
345: from a TV show, based on a novel
346: original TV character
347: from a TV show, based on comics
348: original TV character who has since appeared in comics
349: from a TV show, based on comics; comic version non-villainous
350: from a TV show, based on comics
351: from a TV show, based on comics
353: from a TV show, based on comics
354: from a TV show, based on comics
355: original TV character later migrated to the comics
356: from a TV show, based on comics
358: from a movie, based on comics
360: from a movie, based on comics
361: original TV character
363: original TV character
366: from a TV show, based on comics
367: from a TV show, based on comics
371: from a TV show, based on comics
372: from a TV show, based on comics
373: from a TV show, kind of based on comics
374: from a TV show, kind of based on comics
375: from a TV show, based on comics
380: from a TV show, based on comics
381: from a TV show, based on comics
382: from a TV show, based on comics
387: from a TV show, based on comics
390: from a TV show, based on comics
392: original TV character
393: original TV character
394: from a TV show, based on comics
395: original TV character, though a variation of this character has appeared in comics
396: from a movie, based on comics
399: original TV character, though at least one comic character with the same code exist appeared earlier
401: original TV character, but inspired by a comic character
402; from a TV show; looks like the comic version came first but just barely
406: from a movie; based on a non-villainous comic character
407: original TV character
Adding to what I wrote before:
Bonus: There is one character who got on this list almost entirely due to their name, someone I might have overlooked otherwise. If you find them, you get 20 over limit picks. That is, if you have already picked 30, you can go over by up to 20 more, for a total of 50. You don't have to use them all up at once; you can do 37 one day, 33 another, 40 another (7+3+10). But you have to find that specific character.
The bonus choices can also be used in parts 3 and 4, so if the character isn't found until there are 30 or less remaining, the bonus choices will still be usable.