I seem to be in the minority, but I liked all the redesigns except for the Joker. The black eyes and no lips...eww. ROTJ and JL was a much better look. My favorite of the three DCAU Jokers.
Batman and Scarecrow were the best of the bunch.
I also like how Kevin Conroy changed his voice in TNBA onward. I don't know if it was just natural deepening of his voice over time or if he did it intentionally, but I love it.