In the first Alien vs. Predator film, the humans end up helping the preds kill xenomorphs by bringing them their ancient weapons.
In Assault on Precinct 13 (1976) and its remake, the remaining personnel of a soon to be shut down police station must put their trust on criminals within it to fight worse criminals laying siege on the place.
In Blade II, Blade teams up with the vampires to fight a subspecies of super-vampires that prey on everyone. The vampires end up betraying Blade two-thirds of the way through the movie. Nomak (the lead super-vamp) points out the trope: "Is the enemy of my enemy my friend? Or my enemy?"
Scud: So B-man, what do you think?
Blade: Sounds like a plan.
Whistler: What do you really think?
Blade: They're gonna fuck us the first chance they get.
In Dick Tracy, Tracy considers this trope when deciding whether to accept The Blank's help in defeating Big Boy. Instead, he finally realizes "The enemy of my enemy is my enemy."
This is what prompts the partnership between Wikus and Christopher in District 9. Christopher has spent 20 years collecting enough fluid to power the aliens' buried shuttle so he can take the mothership and get help, but just as he gets the last of it, his shack is searched by Wikus, who accidentally inhales some of the fluid and starts transforming into an alien. On the run from his own company, Wikus teams up with Christopher to get the fluid back from MNU, on the condition that Christopher change Wikus back into a human. It doesn't really work out that way, but by then Wikus has had enough Character Development to be okay with it.
The Sci-Fi movie Enemy Mine (1985) (directed by Wolfgang Petersen), starring Dennis Quaid as a human space marine and Louis Gossett Jr. as an alien soldier. In the midst of an interstellar war between their species, both crash-landed their vessels on a desolate planet and must work together to survive. Years later, after the alien soldier gave birth to a baby alien and died from complications, Dennis Quaid's character raises his adoptive alien son and must protect him and himself from human scavengers who use captured aliens as slaves, until they're both finally found and rescued. It is implied that this event helps to end the war.
Will Smith's character in Enemy of the State pulls an on-the-fly Batman Gambit which ties up two troublesome loose ends by getting them to deal with each other. Through some fast talking and well chosen ambiguous language, he sets up a Mexican Stand Off between a rogue NSA team that has taken him hostage and a gang of trigger happy goodfellas who are looking for a fight. It does not end well for any of them.
Fantastic Four: Rise of the Silver Surfer has the titular team teaming up with Dr. Doom to get the Silver Surfer. Eventually the Fantastic Four team up with the Surfer after Doom betrays them and takes the Surfer's board for himself. And probably after to prevent Galactus from destroying Earth.
In Godzilla vs. Mechagodzilla II, Godzilla and Rodan start off fighting for the unhatched egg on Adona Island, Godzilla because it's a Godzillasaurus egg, Rodan because the egg's presence in the nest he had hatched in made the infant his surrogate brother. When the UNGCC eventually decide to use the newly-hatched Godzilla Jr. to lure Godzilla into a fight with Mechagodzilla, the two monsters get mortally wounded, and Rodan sacrifices what little life he has left to revive Godzilla.
In Godzilla vs. Space Godzilla, M.O.G.U.E.R.A. is built as yet another anti-Godzilla machine. But when SpaceGodzilla lands in Fukuoka and starts growing a large mass of crystal across the surface of the city, the M.O.G.U.E.R.A. team ends up having to work with Godzilla to bring down the extraterrestrial invader. This trope is especially applicable for Akira Yuki, the M.O.G.U.E.R.A. captain who had been working to kill Godzilla as revenge for the monster killing his best friend Goro Gondo in Godzilla vs. Biollante.
The first half of The Good, the Bad and the Ugly is a slowly-escalating buildup of hatred between Blondie and Tuco to the point where they're inches from clawing out each others' eyes. Then Tuco learns the location of a graveyard where gold is hidden, Blondie learns the name on the grave where the gold is buried, and they're forced to work together, later uniting against Angel Eyes after he learns Tuco's half of the secret.
Hell in the Pacific, about an American and a Japanese soldier trapped on an island together, and which inspired the film in the previous entry, natch.
The film Krull begins with this, as two rival kingdoms arrange a political marriage to unify them against the alien invasion. Sadly, it does them little good as the highly advanced Slayers storm the castle and kill everybody except for the heroic prince and his future bride, who is taken by the invaders.
The Matrix Revolutions. Neo and the Machines must work together to destroy Smith before he takes over both the Matrix and the Machine World. After Neo allows Smith to possess him, the Machines use their power through Neo's body to destroy all of the Smith clones.
In the climax of Mean Girls 2, Jo's former friends decide they hate Mandi more than they hate her and agree to help her.
Kind of lampshaded in Ocean's Thirteen, when they decide to include Benedict in their plan:
Linus: We've shaken every tree... Rusty: I really wanted to avoid it this time...
In Once Upon a Texas Train, the retired outlaws and the retired Rangers are forced to combine forces to combat a gang of younger, more ruthless outlaws.
In the Pirates of the Caribbean franchise, every character views the others as either enemies or incredibly stupid pawns, but will readily concede to work together when their priorities mesh. These unholy alliances tend to confuse casual viewers, who are convinced (très incorrectly) that the adversarial role Barbossa plays in the first film completely contradicts the compatriot role he plays in the third.
Mentioned in Predators when Royce tells Isabelle that he intends to free the captured Predator and use that momentary trust to have him find the predator's ship and escape. Isabelle then adds:
Royce: The enemy of my enemy...
Isabelle: That doesn't make it a friend.
A very short alliance happens in Raiders of the Lost Ark, when Indy and a mook are struggling over control of a gun, when Toht says "Shoot them — shoot them both", and suddenly Indy and the mook cooperate to shoot the other mook pointing a machine gun at them.
In the end of Resident Evil Retribution, Alice has to work with Albert Wesker to ensure the survival of the last of humanity against the Red Queen.
Balthazar and Mathayas resort to this in The Scorpion King in order to take down Emperor Memmon.
Shakespeare in Love: When the Master of the Revels orders the Rose Theater closed indefinitely, thus preventing Shakespeare and company from premiering Romeo and Juliet, Richard Burbage, owner of rival theater The Curtain, makes a peace offering, saying that they should stand together against their common enemy:
"The Master of the Revels despises us all for vagrants and peddlers of bombast. But my father, James Burbage, had the first license to make a company of players from Her Majesty; and he drew from poets the literature of the age. We must show them that we are men of parts. Will Shakespeare has a play. I have a theater. The Curtain is yours."
Thunderball. During the big underwater fight at the end, when sharks start to show up the SPECTRE frogmen and their opponents stop fighting each other and start attacking the sharks together.
Subverted by Transformers: Dark Of The Moon. Prime and Megatron teaming up to battle a greater threat is fairly common in Transformers media, but this time when Megatron offers a truce, Prime responds by cutting his head off.
West Side Story: Despite their hatred of each other, the two gangs seem pretty united in their hatred of the cops—the Jets laugh when Bernardo mouths off to him, they pretend to be buddies to avoid suspicion, and when Shrank insults Bernardo, it's Riff who hold him back from attacking him.
In The Wolverine Harada cites Viper as a "means to an end," and voices his displeasure towards her consistently. Viper seems indifferent to Harada attitude-wise, but she just sees him as another inferior underling.
In The Wrong Arm of the Law, the tactics of an IPO mob from Australia ends up making strange bedfellows of not only underworld rivals, but also the underworld itself and the police.
The entire point of X2: X-Men United: the X-Men team up with Magneto and Mystique to stop a human villain from killing all mutants.
Right up until Magneto and Mystique decide to invert the attack and have all the non-Mutants killed instead.