I am a huge fan of Hero Points in almost every system that uses them. I love having tokens that the players can have and spend to help them be more awesome. I love how the economy of them allows me to flat out bribe the players for playing to the theme and genre of a game by rewarding heroic actions. I also love that they let me 'pay' the PCs when I do fiat against them specifically to make things more interesting.
One thing I really like about Hero Points though, is that if the 'heroes' get points to help them be more heroic why can't I give the Villains 'Villain Points' to help them be more villainous?
A Special Kind of NPC
Now I don't mean any adversary to the PCs when talking about villain points. I mean the main antagonist. The counterpoint to the heroes. The planners, the schemers, the masterminds. The adversaries and antagonists that make the plots happen and live to foil the actions of the heroes who are trying to foil their own plans.
They Basically Work Like Hero Points
Beyond that, the idea is for 'Villain Points' to work like Hero Points. They can be used to improve a roll, to make rolls against the villain harder, or for other minor benefits. If your system has rules for Hero Points, you can basically use those in reverse for the villain. Just remember, Heroes should use theirs to be more heroic; villains should use villain points to be more villainous.
Some Extra Bells and Whistles
Beyond the inverse of Hero Points there are a few things that I like to always have in place for Villain Points. Those are as follows:
Win A Tie, Or Otherwise Seize Initiative
Villains need to challenge heroes, and sometimes that means they need to be able to act. By spending a Villain Point the villain can go 'now' this round. This can be used for just this round, or when setting initiative for the whole combat. A 'softer' use of it is to spend a villain point to disregard normal tie break rules when two characters get the same initiative and instead use it to choose who goes first.
Escape A Scene
Plans go wrong. Things go dangerous. This is especially true when PCs are around. By spending a Villain Point the villain is able to escape. It is up to you if the villain has to break line of sight or do something else to make this viable. The point here though is that villains - smart ones at least - should have an escape plan, and this point lets them enact it to get out of dodge. This does not work for their group, just the villain. The idea isn't to rob the PCs of a victory, just so they don't get a total victory and take the villain down. Also of note, a villain shouldn't be able to use this in their home base, or when otherwise cornered by the PCs. If the players set up a great ambush or trap, let them play it out. But if the PCs are jumping into the villains game without a plan or setup? Well, a good villain always has an escape plan.
Activate a Contingency/Summon Help
A villain can use a Villain Point to activate a contingency plan, set something in motion, or otherwise bring help to bear. This is effectively spending a villain point to change some aspect of the situation. The building goes from being a building, to being a building on fire or collapsing. It can bring in more allies to help. I especially like using this to provide the cover needed for the villain to escape a scenario.
The Right Gear
Some systems have this by default, but sometimes a villain needs a piece of equipment and just doesn't have it on them, or you forgot to put it down. Spending a Villain Point lets you correct for that mental hiccup in a way that has some mechanic for it. This is the same thing as just saying they have it - the PCs don't get to know - but it also shows the appearance of fairness which can be more important in some situations.
It also helps overcome problems of "just how much stuff does this person have on them" since the point is being spent.