Poison Ivy used to look slightly like Jessica Rabbit. Now she looks more like an elf with pale green skin.
The Penguin's body used to be deformed, giving him bird-like qualities. His new design makes him look more human and less hunched.
The Mad Hatter's age changed from middle-aged to elderly. His facial features and height were altered giving him a more rat-like look.
The Riddler had red-hair and wore a green suit with a purple mask over his eyes. In his new look (which I think is worse) he has a slender body and wears a jumpsuit, which adds a dash of boldness.
The Ventriloquist lost his hair and got new glasses and eyes. His boss, Scarface, became more square-like.
Both Two-Face and Bruce Wayne's design weren't changed too much, but for some reason it hurst my eyes seeing them in a different art style.
From what I've seen, the only two characters in the series that had their designs edited more than twice are the Scarecrow and the Joker.
The Scarecrow didn't look really scary at all when he first appeared. Even when they edited his mask with hair and added pupils, he still didn't look terrifying enough. Now in The New Batman Adventures, Scarecrow went from looking like the one in The Wizard of Oz to now the Chainsaw Massacre.
As for the Joker, he originally looked more similar to the comic book version, but then was given a pointier chin and edges. The only slight problem with his makeover was that his eyes looked too beady-like and he's missing his zany lipstick. This change was corrected in Batman Beyond: Return of the Joker where his features from both designs were rolled together into one package. The result was perfect.
Source of all images above from: The World's Finest.
Batman belongs to Warner Bros./DC Comics.