Because the villain always explains his plans, one villain per session can be compelled to reveal his plans or goals through a monologue, at no Fate point cost to the player who proposed it.
Villain monologues are a staple of four-color comics. This stunt allows players to more easily take advantage of such distracting speeches to undo the villain's plan.
Because the final fight against a villain should be a big brawl, during such a fight each character can use the "Collateral Consequences and Extreme Effort" optional rule once in the session.
Some games like to have a flashy final battle, where a villain who was wiping the walls with the heroes finally gets his comeuppance (and the city gets soundly trashed). The GM can declare this stunt to be in play during the session when the players are ready for this big showdown.
Because the first defeat from a villain rarely leaves lasting consequences, the first time characters offer a concession to a villain, they erase any consequences inflicted by that villain.
A staple of certain games is the "unbeatable boss fight" - the one where the GM gets to establish just how tough his villain really is. To soften the blow of this first meeting, the GM can allow this stunt.
Because the status quo is generally preserved, players can use their minor milestone to clear either a Moderate or a Severe Consequence instead of changing their stunts, aspects, or approaches.
In episodic games, it is common to enforce a status quo - the hero is always after his girlfriend to marry him, the villain has always sworn vengeance on the hero, major injuries or life-changing events don't happen, and so forth. In these games, you can hit the reset button on many things, the most common being Consequences taken, at the end of the story.