The only moments Wonder Woman's villains appeared in the book was:
When Cupid showed up to test how great and deep his love for Wonder Woman was despite Cupid not being close to Wonder Woman;
When Apollo - one of the primary big baddies of the Wonder Woman's book and that in it wanted nothing to do with her - showed up to act concerned about Wonder Woman dating an alien receiving a huge beating from Superman showing how awesome and powerful Superman was;
When Superman was turned into a beast by Circe and Wonder Woman was forced to save him without resorting to killing because the whole moral of the story was that she used to be uncaring and murderous and thanks to Superman's influence learned to be a better person and hero;
When Wonder Woman begged the gods to heal Superman prompting them to test him to see if deserved and of course he passed all the tests because he's that awesome.
So everything revolved around Superman even when dealing with her villains. Other than those moments pretty much all the other arcs and specially the cross-overs were about Superman's problems and villains. Them against Doomsday and Zod/Faora - where Superman saves her -, them against Brainiac, Mongul, etc - where she's constant support mode -, them against Vandal Savage and his children - where again she's in constant support mode.
There wasn't one single arc that was about Wonder Woman. That deal with her issues. SM/WW was a Superman book where Wonder Woman playing the role of sidekick/love interest.