7. Kerrigan & Raynor (StarCraft series)
The Starcraft series boasts a lot of characters, most of whom don't agree on too much (thus all that warring). But one thing most of them have in common is a good strong hatred for Kerrigan. Former love interest Jim Raynor is somewhat conflicted about helping Kerrigan out after she pointedly betrayed them and killed his Protoss buddies as thanks for helping her out of a jam in the expansion. Also she's killed like billions of people (with a b, Jim! A b!). But Raynor opts to put his unhealthy relationship with his mutant girlfriend first and sides with her against foes both human and alien. And after all that effort to turn her human again, she up and decides to go back to being a Zerg (though who could argue with such perks as "purplish carapace skin," "medusa tentacle dreads" and "legions of unstoppable space monsters at your command"?). Yet even after this, Raynor can't seem to stay mad at her even though she has literally murdered most of his friends. Jim, you do realize there's an entire galaxy of other women out there?
At least until Kerrigan kills most of them
6. Frog & Magus (Chrono Trigger)
The cool thing about the Magus & Frog team-up is that it's entirely optional. If you happen to hate the cackling evil wizard enough you and your party can just finish him off and get sweet, sweet vengeance for poor mutated Frog. Of course, if you do decide to murder the guy you'll be missing out on having yet another magic user in your party. And you'll miss out on some unique dialogue options. Gotta love those. Also, most important of all, if Magus dies by your player's hand, you'll never have the satisfaction of resolving his quest to save his sister, the all-consuming goal that led him down a slightly sinister path in the first place. Oh, wait, that never gets resolved anyway. That's rough. You should probably just kill Magus. Spare him the pain.
5. Sonic & Eggman (Sonic Adventure 2)
In a video game world where plumbers and dragon-turtles can be depicted as natural enemies without anyone questioning it, can we really be surprised that Sega's premiere franchise would pit a blue hedgehog against a Teddy Roosevelt look-alike? Sonic and the evil scientist have gone more than a few rounds over the latter's fiendish plots to take over the world using egg-shaped devices, but old rivalries are put aside when an even greater evil rears its even uglier head. Sonic Adventure 2 not only gave players the chance to play as the good (bad) doctor, but had the duo teaming up with their respective pals. Does this mean the player gets to power through levels with the assortment of large automatons, robotic henchmen, and giant airships ritually employed against Sonic? Well, no, those devices are strictly anti-hedgehog in nature. But you do get a laser gun! And the chance to shoot Tails with that laser gun! So it all works out. Eggman's villainy ranking may have fallen to the point where a two-tailed fox is considered a worthy rival. But as long as future team-ups between Sonic and Eggman don't preclude the possibility of someone firing missiles at Tails, I won't complain.