I have been reading Masks: A New Generation lately. The game didn't have to do much to catch my eye. I'm a sucker for super hero stories and games, and even more of one for teen heroes. Something about the teen hero part of super hero stories just really speaks to me I guess. Anyhow, Masks is a Powered By the Apocalypse game in the same sense as Dungeon World and Monster Hearts. This means the game is focused on quick action with simple resolution that keeps things going. It also means that the game is more interested in the emotional reality of what is going on than the physical reality.
It's a good system, but the thing I like most so far is the section on creating villains. Namely, the part I've more or less paraphrased in the title of this post about villains and their goals. It's a great reminder, and also a big key to making your villains ones that will be remembered.
But I Want To Destroy The World
Many of the "cliche" villain goals don't have much 'human' about them. Subjugate the masses, rule with an iron fist, and blow up the world aren't things someone in grips with their humanity would do, and that's ok. There is room for those goals and threats. Just realize that what you're doing there is putting your PCs up against a monster, not a villain. This is fine, but remember: monsters can be awesome, but villains get remembered long past their story being forgotten.
How Do They Remain Villains?
So you have a "human" goal, how does your villain remain human? Well, the big difference between a Hero and a Villain is how they go after their goals. A hero will act reactively, defending their goal against that which threatens it and trying to light the way towards a better path. A villain? A villain is a lot more pro-active.
To get the point, let's look at some classic villains. Magneto from the X-Men is a villain with the goal that he will not let what happened to the Jewish people in Nazi Germany happen to Mutants. To achieve this goal he has become a Mutant Supremacist who makes moves to strike down the military arms of humanity and put Mutants on top. By comparison, Professor Xavier wants to work with humanity. Both men seek a world where mutants are free to live their lives in the open, but how they're going about it is very different.
In Arkham Asylum Joker states his goal to Batman. He just wants Batman to see the world the way he does: giggling and bleeding in the corner. In effect, Joker here just wants someone to understand his viewpoint. What that viewpoint is may change, but it's a theme that runs with Joker in numerous incarnations, and frequently in ones that pop up on "best Joker story lists."
Some Other Examples
Almost any place a story goes bad can be the birth of a villain provided the villain is willing to make sacrifices to achieve their goal.
A character who wants nothing more than to see their fractious Empire united may become a villain and threat so large that the Empire must unite to withstand them.
A scientist who regrets not making the action that ruined their life and cause their best friend to commit suicide could be making a machine to go back in time and fix that mistake. They just need money and equipment to get started now.
A fallen hero may just want to protect the masses but has become jaded with how the courts work, and so now they're killing villains that cross a certain line and you can either join them or get out of their way.
A normal person may be trying to kill heroes because he's trying to avenge those who die in the crossfire when super-powered beings throw down.
Human Goals Make Emotional Resonance
the reason you want these human goals is two fold: first they make the character more interesting. Second, they make the character relatable.
Give your villain a proper goal and reason, and the PCs/Heroes may become conflicted. Some may not think it's that bad. Some may be tempted to join. Even those who aren't may not be happy with their victory after.
All of this makes for great stories and better campaigns. Give it a shot.