The ‘villains’ are fairly complex in Orpheus Ruse, Metahuman Inc., and the two Deathless books, I think, partly because the choice of who is and who is not a villain is partially the players’.
I also liked the antagonists in Study in Steampunk, where there are definite motivations, though that game is gender-locked male.
A lot of the titles do seem to have more antagonists than villains, so the people you may or may not be working against aren’t necessarily bad, depending on the PC’s point of view—but they can certainly be working against your character.
Slammed! and Tin Star also have really solid antagonists, but who they are might depend on how you play (particularly in the latter), and I wouldn’t necessarily call all their antagonists villains, either.
Edit: @CorporalHam You might want to use spoiler tags when describing the motive and style of villainy in specific titles, in case people haven’t read them yet.