Sonic Underground gave us Sleet and Dingo, a pair of bounty hunters Robotnik hired to take down Sonic and his siblings.
In the second season of Adventures of the Gummi Bears, Duke Igthorn is given some ogres that are different from his normal unnamed Mooks: Gad (who is purple) and Zook (who's green with orange hair). The two are always seen together and, as the series progresses, becomes much more prominent.
Professor Pyg and Mister Toad in Beware the Batman. According to Word of God, they're a direct homage to Mr. Kidd and Mr. Wint from Diamonds are Forever.
Bump in the Night featured a pair of aliens named Sleemoth and Gloog as minor recurring villains, who would try to invade Earth in each of their appearances only to be humiliatingly defeated by Mr. Bumpy, Squishington, and Molly Coddle.
Hey Arnold! featured a pair of crooks constantly seen together named Vic and Morrie.
Invader Zim: Almighty Tallest Red and Purple. An interesting example, because they're technically the Big Bad Duumvirate, but since Zim is the main villain trying to take over the Earth they mostly just act as MacGuffins, exposition or comic relief.
This is probably because they're not actually particularly interested in conquering Earth; on the big map of the galaxy where they've got Operation Impending Doom Two laid out, Earth is a post-it note stuck to one side.
Bebop and Rocksteady at times fell into this role in the 1987 series.
In the 2012 series it's Chris Bradford and Xever, who get mutated into Dogpound/Rahzar and Fishface. In season 2 the show adds Anton Zeck and Ivan Steranko, who get mutated into its incarnations of Bebop and Rocksteady.
Badlands Meeney and J. Skulking Bushwhack from Terrytoons' The Adventures of Lariat Sam.
And various pairs like Rumble and Frenzy and all of the Decepticon Targetmasters, Headmasters, and Duocons, the G1 Scorponok and his partner Lord Zarak arguably being the most iconic example.
Transformers Animated also has Blitzwing and Lugnut, who tend to hang out together even when they aren't actually fighting anyone. The funny thing about that is, because of Blitzwing's near-Literal Split Personality, they can either be brains and brawn (Lugnut and "cold" Blitzwing), brawn and brawn (Lugnut and "hot" Blitzwing), or brawn and WTF!? (Lugnut and random Blitzwing).
Perhaps most emblematically, Spaceshot and Blackout, the mismatched pair who operates one of the most powerful weapons of the Decepticons' entire fighting force, the Decepticon Anti-Aircraft Base. Spaceshot is dutiful, dedicated, and heroic (yes, there are heroic Decepticons), while Blackout is a cowardly, spineless, would-be deserter. What's more, as Micromaster Combiners, they each transform into one half of a vehicle mode, with the other one turning into the other half.
And every incarnation of the Dreadwing and Smokescreen molds from G2, including the originals, BB and Starscream from Beast Wars II, Gigant Bomb and Smokesniper from Robot Masters, and Smokejumper and Dreadwind from Robots in Disguise and Armada. While the various incarnations have their idiosyncracies, the constant is that they're Brains and Brawn who pal around to cover up their weakness in either area.
Similarly, the original Dreadwind and Darkwing, as well; Like Dreadwing and Smokescreen, they can also combine. (Their combined form is called Dreadwing, but isn't to be confused with the other Dreadwings. Well, not all of them, anyway.) Also, Dreadwind and Darkwing each has an organic partner who powers them up. However, they don't get along with their partners so well.
#21: Could you sign this, boss? It's for 24, he got knifed by the Moppets. The Monarch: Which one is 24 again? #21: What?! You're kidding, right? Let me give a hint: you know how every time you talk to me, there's usually another guy next to me. That's 24. The Monarch: Right, right, right, the one that sounds like Ray Romano. I like him.
Just any duo voiced by Hammer and Publick might qualify for this.
Inverted by Mr. Doe and Mr. Cardholder, the OSI operatives sent to Jonas Venture, Jr. to help defeat The Monarch. And then played straight in the Season 4 finale when it turns out they are Guild moles.