Assuming you're counting stories where the villain did very bad things for the purpose of a doing something good, there is an anime from 2005 called Speed Grapher.
Oof that was a hard one to watch sometimes
Despicable Me?
The Good Place, season 2.
"Villains by Necessity" by Eve Forward.
The Sixth Day, one of Arnold Schwarzenegger's please-take-me-seriously projects, is possibly the wrongest it is possible to be about whether clones are people. Still a fun movie. Just ass-backwards in its motivation. I'm not sure how much of its moral grey area was intended by the script or the direction. The anti-clone "good guys" are pretty terrorist-coded. Arnie's just caught up in the middle of their guerrilla fight against a generic corporate bad guy. Who solved death. How terrible.
Off-topic Schwarzenegger faff: End Of Days is dumb. Jingle All The Way is the most 90s Christmas movie possible. Eraser is a slick action movie that somehow has no cultural cachet outside of every video game with a railgun.
Sophia, Garden of Eden, Genesis
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