The character designs were handled by Bruce Timm, but many contributed to those final designs, including artist Kevin Nowlan. Nowlan and other artists like him would submit their designs to Timm, Eric Radomski, Paul Dini, and others so they could change and tweak as needed, and you can definitely see the influences in Nowlan's sketches at the time.
"I think Bruce Timm had seen my Man-Bat Secret Origins story and made note of the pared-down style I was using," Nowlan told 13th Dimension. "I remember him talking a little about how the heavy rendering approach that other Marvel and DC artists were using at the time just wouldn't work with cel animation. Everything had to be reduced down to the bare essentials, which lit a fire under me because that was my obsession at the time."
Nowlan would take those notes and run with them, delivering sketches for characters like Batman, Manbat, The Ventriloquist, Killer Croc, Joker, Catwoman, Robin, and more.
"As a challenge. "How can I say as much as possible with just a few lines?" I tried to focus on personality with the supporting cast and the thugs," says Nowlan. "For some, Bruce would suggest a real person as a starting point or inspiration. A tough little gun moll (Jesse) was based on Rhea Perlman. The Ventriloquist was based on George Will."
The designs were as simplistic as possible, with no fine lines or crosshatching. He would give this makeover to villains like the Penguin and Riddler, who were unfortunately not used in the final version.
"The Penguin was changed to the Tim Burton movie version. But I hadn't done much more than sketch the '66 TV character so I didn't have a lot invested in that one," recalls Nowlan. "I also had Frank Gorshin in mind when I drew the Riddler. The Mad Hatter always looked very awkward to me. I was thinking of the toothy, chinless, Tenniel drawings from the original book. In the end, it didn't matter because Roddy McDowall did the voice and just acted up a storm. No one noticed the character design, good or bad. They were focused on Roddy's virtuoso performance."
While the final designs would be a bit more angular in nature, characters like The Joker and Robin are almost exactly as Nowlan sketched them. You can view these designs and more in the gallery.