1. \[Hazbin Hotel\] Most sinners in Hell are bad people who do bad things, but most of the people they hurt are either sinners in Hell or the exterminators from Heaven. There are exceptions, but this is the case for most of them.

2. \[Infamous\] In the video game Infamous, your Karma can range from Hero to Infamous, but the enemies you face in story missions are exactly the same either way. You are given choices and optional side missions that let you hurt innocent people (you can even go around killing innocents for no reason if you want to), but you don't technically need to cause intentional harm to a single innocent person to be considered a bad guy by the narrative. 

Later games in the series tend to give choices that impact the story more, though you still primarily fight villains in the main plots even if you are evil.

3. \[Overlord\] In this highly underrated game, you play as an evil Overlord conquering various lands. However, the enemies you face are almost all either outright evil, corrupted beyond help, or mindless, and in one cast outright beg you to kill them. The game has a morality system (0 to 100% corruption), but you are still considered evil in the story even if all the civilians love you because you are nothing but helpful to them. It's excellent DLC, Raising Hell, addresses that by mandating various evil actions (such as burning innocent people alive), but you are still doing these actions to face an evil threat.

Overlord 2 changes the morality system to instead be a scale of domination and destruction; choosing to kill everyone (destruction) or magically enslave everyone (domination) are both unequivocally evil. You still fight lots of villains, though.

[Mixed Trope] Villains who almost entirely fight or kill other villains or evil characters.