Biggs and Wedge in Final Fantasy VIII. Who suffer demotions after every encounter, until they quit in late disk 3. Biggs and Wedge are your teammates in early Final Fantasy VI. Considering you were being controlled and they worked for the ones who did it....
Logos and Ormi, the co-dragons to LeBlanc in Final Fantasy X-2, with special emphasis put on the aspect of them being nearly complete opposites of each other. Logos is tall while Ormi is short, Logos is skinny while Ormi is fat, Logos is one of the smartest villains in the series to date while Ormi is one of the dumbest, Logos has a calm and collected personality while Ormi is impulsive and easily excited, Logos speaks in a low monotone and rarely raises his voice while Ormi's usual tone is screaming at the top of his lungs, Logos uses a pair of ranged weapons in battle while Ormi uses a single melee weapon, Logos favors a battle strategy of inflicting multiple status ailments to slowly wear down his enemy while Ormi favors a strategy of overwhelming his enemy with brute force. About the only things they have in common are their fanatical loyalty to LeBlanc and their willingness to do everything in their power to ensure that her plans succeed.
The Kirby series has recurring bosses Mr. Shine and Mr. Bright, an anthropomorphic moon and sun that usually attack Kirby in tandem.
Jasper and Frank from Fallen London. Two Unfinished Men, AKA amoral Golems, that are a bit wiser and more cultured than most of their kin. They're supposed to be agents of the Masters of the Bazaar, but most of the time they just kind of do their own thing, sometimes even requiring extensive (attempts at) beatings to get them to go back to work.
Rip and Shred from the SNES classic, Rock 'N Roll Racing. They don't have much personality beyond being Palette Swap twins and buying their way into every race, but they'll try to kill you dead just like everyone else. They are also terrible racers, given they always come in 3rd and 4th place (and there are only four racers competing at any given time).
Fire Emblem has had a good many of them, all looking quite similar to one another (the second set actually an outright Palette Swap of the first, as they were still on the same system, one of the few character portraits to be recycled across multiple games). Sealed Sword started the tradition with Maggie and Rose; Blazing Sword carried it on with Jasmine and Paul; Radiant Dawn continued it with Pain and Agony; Awakening carried on with Vincent and Victor; and Fates kept it going with Lloyd and Llewelyn. Defining traits are that they're generally quite effeminate despite being large, baldGonks, they're bandits unaffiliated with any of the actual villains of the story, and they're invariably of axe-wielding classes (except for Pain and Agony, who were tiger laguz). Victor and Vincent were the only pair not fought as a Dual Boss, while Lloyd and Llewelyn were the only pair to be playable if captured.
Girtar and Sardías in Third Super Robot Wars Z: Tengoku-hen, kind of seem like comic relief characters. At the very least, they're portrayed as being a lot more bumbling than the other Sidereal members thus far.
The mid-90s iteration of Where in the World Is Carmen Sandiego? had this in the form of two klutzy janitors working for Carmen whom the player could sometimes see trying to clean up after a suspect passed through; usually with hilarity ensuing. They were usually a cue to the player that they were on the right track. They get apprehended along with Carmen during the final showdown between the A.C.M.E good guides and Carmen herself at the end of the game, provided that the player is able to find her in time, of course.
Overwatch gives us Junkrat and Roadhog, a pair of Mad Max inspired Australians out on an international crime spree. Their main goal appears to be keeping a firm hold on whatever unknown secrets Junkrat found within the wreckage of the Australian Omnium, Roadhog tagging along as a bodyguard who receives 50% of the spoils.
Bravely Second has Sergeant Sapp and Private Piddler. Even if they're responsible for two very difficult boss fights, it's hard not to find them endearing.