I loved each of the times Superman outsmarted Mister Mxyzptlk in the S:TAS episode "Mxyzpixilated". It's great to see that Clark can be clever as well as powerful.
The fight between Superman and Captain Marvel in Justice League: Unlimited was amazing. I loved every bit of it: the manipulation by Lex, the destruction of the city, the media catching it all, and the public getting even more scared of the Justice League. This was a simply amazing episode as well.
But for me, the ultimate Superman fight in animated form happens when he and Supergirl fight Darkseid at the end of Superman/Batman: Apocalypse. I can watch that fight over and over again.