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.
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.
In Phineas and Ferb The Movie: Across the 2nd Dimension, there is an alternative version of the show's Big Bad Dr. Doofenshmirtz, who is far more competent and successful than his original counterpart, as he defeated the alternate Perry the Platypus by turning him into his loyal sidekick, took over his Tri-State Area with an army of hovering robots, and ruled it with an iron fist for 5 years.
In the episode sequel Tales from the Resistance: Back to the 2nd Dimension, the alternate Doof's wife (the alternate Charlene) counts as well, as she managed to turn several animal agents into cyborgs to enforce their reign and later help Doof escape from prison in case he was overthrown. Special points also goes to their daughter (the alternate Vanessa), who managed to formulate a clever escape plan for her family in case they face arrest for their crimes against humanity.