That list didn't count webisode appearances, but for the sake of efficiency:
Heroes
Batman - 53
Superman - 39
Wonder Woman - 32
Cyborg - 17
Plastic Man - 13
Firestorm - 11
Green Arrow - 10
Zatanna - 8
Space Cabbie - 7
Shazam - 7
The Flash - 7
Booster Gold - 10
Hawkman - 6
Constantine - 5
Green Lantern - 5
Stargirl - 8
Swamp-Thing - 5
Atom - 5
Martian Manhunter - 5
Supergirl - 4
Vixen - 3
Etrigan The Demon - 3
Blue Beetle - 3
Mr. Terrific - 3
Dr. Fate - 2
Red Tornado - 2
Big Barda - 2
Krypto the Superdog - 2
The Wizard Shazam - 1
Jonah Hex - 1
Bizarro - 1
Mr. Miracle - 1
Dr. Light - 1
Black Canary - 1
Uncle Dudley - 1
Streaky the Supercat - 1
Mark Hamill - 1
Villains:
Lex Luthor - 9
Joker - 6
Lobo - 5
Poison Ivy - 4
Harley Quinn - 4
Felix Faust - 4
Darkseid - 4
Granny Goodness - 4
Toyman - 4
Solomon Grundy - 3
Mr. Mxyzptlk - 3
Hive-Master - 3
Penguin - 3
Black Adam - 2
Brother Night - 2
Klarion - 2
Brainiac - 2
Calculator - 2
Mr. Mind - 2
Riddler - 2
Desaad - 2
Kanto - 2
Gorilla Grodd - 2
Chronos - 2
Zod, Faora, and Quex-Ul - 2
Atrocitus and the Red Lanterns - 2