Yeah, is a tricky one. But the trick is to make them stand out in some way from his minions.
Here are some ideas on how:
1-Competence and results: They may not get their hands dirty very often, specially if they are trying to hide their presence, but when their hands get dirty.....o my, things get messy very fast......he doesn`t stop to monologue, if he manages to get tricked, he doesnt fall for the same trick twice, he can adapt when things go out of plan, things like that.
Ex:"did he managed to kill a member of the main cast, corrupt another one AND conquer the whole city, doing all this with lots of style.....???.....holy shit........what a badass."
2-Characterization....Well this goes to every named character that is relevant to the story, but give them a compelling and memorable personality. This helps with building their strenghts and weaknesses too.
3-Motivations: why do they do all this stuff?, a generic doomsday villain may be forgotten quickly, but someone with more interesting reasons?.....this can be way more entertaining.
4-Design: if they look cool, imposing and badass it helps a lot. No two badasses are the same, it depends a lot on what you are aiming for. Do you want him to be scary?, do you want him to be charming?, imposing?, elegant?, tough looking?, intimidating?, a deceiving apperance?, a comination of these and other traits?