Here are some examples I like that haven't been mentioned yet (and I'm excluding sequels, since - as Marc Bodnick mentioned in his answer - this is a common trope there):
In the video game Super Mario RPG, longtime antagonist Bowser joins up with Mario to face down a new enemy who has shown up in the Mushroom Kingdom (and taken over Bowser's castle in the process).
In the 14-part Maximum Carnage storyline from the Spider-Man comic books, Spidey's former foe Venom teams up with the web-slinger to try to take down Carnage, who is the more powerful offspring of Venom himself (Spidey fans: Yes, I'm paraphrasing/simplifying a lot; forgive me).
In the recent remake of the video game Splatterhouse, college student Rick teams up with a sadistic supernatural entity of death and mayhem possessing an ancient mask - because the two of them need each other to stop a Lovecraftian cosmic abomination from entering (and thus destroying) our world.
In the video game Grandia II, the dark god Valmar is in pieces, and is trying to be reborn. The pieces each have minds of their own, and one of them - Millenia, who is the incarnation of Valmar's Wings - teams up with the heroes to stop the other pieces of Valmar (initially just because she wants to consume them and gain their power for herself, but later on because she decides that reawakening Valmar isn't such a cool idea).
In the storyline behind some of the recent Magic: The Gathering trading card game products, a vampire named Sorin Markov - born to vampire nobility on a world where humanity is mostly prey to monsters - allies himself with humanity against the monsters, and even uses his magic to create a powerful archangel to be the champion of humanity (granted, he does this initially because he worries that the vampiries of the world will eventually "overhunt" humanity to extinction - and starve themselves to death and/or destroy the world in the process).
In the movie Constantine, starring Keanu Reeves as the eponymous supernatural private eye, the Devil himself shows up to help Constantine save the world (mostly because the world was about to be ended at the hands of the devil's son, and the devil had wanted the world for himself) - the whole finale of this film is, frankly, what makes it worth watching, and is most of the fun-to-watch and well-done twists and conclusions to a film I've seen in a long time.
In the video game Darksiders, the character Samael - implicitly the recently-dethroned lord of Hell - helps the hero reach and kill the Destroyer, who usurped lordship of Hell, wiped out humanity, and laid siege to Heaven. His reasons are initially cryptic, but it is ultimately explained (somewhat) that this was because of a combination of wanting more power for himself (he has the hero help him out in exchange for his support), wanting revenge upon the Destroyer, and distrusting some of the secret antagonists that enabled the Destroyer's rise to power.