Megamind is completely based around this trope. The entire plot of the movie begins with our supervillain fighting his superhero nemesis like always, but then he actually manages to win, and the hero dies. Nobody comes to save the town, the villain takes over, and everyone is sad, however the villain comes to wonder what to do next. The rest of the film is basically what might follow with the villainsuddenly not having an arch rival.
At the end of Cars, villain Chick Hicks wins the final race of the season. Subverted because Chick would never have won fairly; he had to run one of the racers off the road, totaling him, and McQueen deliberately lost the race to help said guy. Chick is booed off the stage for being a dirty cheater, and doesn't get the sponsorship contract that normally goes along with winning said race. In other words, a Meaningless Villain Victory..
The first half of "The Lion King'' ends with Scar successfully killing his brother (though admittedly the plan fails to kill Simba), taking over the Pride Lands, allowing the hyenas to enter said Pride Lands, and successfully persuading Simba to go into exile.
In Despicable Me, the Villain Protagonist succeeds in stealing the moon. Then again, it soon returns to its proper place. On the lighter side of things, he is actually considered to be a hero for doing so.
Pinocchio averts this trope with Stromboli, Lampwick and Monstro, but plays it straight with "Honest" John Worthington Foulfellow, his sidekick Gideon, and the Coachman, who all win (though in the Coachman's case this is because nobody opposes him). In the Video Game however you actually fight the Coachman where he gets a Disney Villain Death.