A good 'enemy' to throw against players, especially bloodthirsty or capable ones, are organizations. So yeah, they use cults a lot, and royalty, who would also have a wide array of underlings at their disposal. It is a good way to prevent characters from completely destroying a threatening powerful enemy all at once with lucky rolls or clever thinking.
That ONE evil wizard you had against the players? Well they caught up to him and disposed of him in quick fashion, much to your surprise an chagrin. Now what? If you have a circle of evil wizards though, there can always be another enemy to stand in the way, until such time as it feels right to end the adventure.
I mean sure you can make up reasons for not being able to find or kill the solitary bad guy, and really there is nothing stopping you from having a head of an organization or cult die to the players. The organization behind them just ensures you have a ready to tap pool of like minded villains.
I think a lot of others offered some good reasons and thoughts as well.
So for me it will never be just Bob from accounting, but the whole accounting department!