Darkseid wasn't really a Superman villain until TAS made him one. And the reason they made him one was because Superman simply didn't have any top-tier arch-nemeses once you got past Luthor and Brainiac.
Actually, Darkseid's first appearence was in an issue of Superman's Pal Jimmy Olsen
-#134 (November 1970). So yes, he could be considered a villain of Superman's.