Scratch and Grounder in Adventures of Sonic the Hedgehog with Robotnik as the higher up. Sometimes Robotnik himself joined them, and led from the front. Semi recurrer Coconuts also joined the team on occasion.
The pet store employees in the American Dad! episode "The Full Cognitive Redaction of Avery Bullock by the Coward Stan Smith".
Walter Wolf, Sid the Squid, and Beanie the Brain-dead Bison, Slappy Squirrel's archenemies on Animaniacs.
Though not villains, Sissi, Hervé, and Nicolas from Code Lyoko qualify at their most antagonist (or when possessed by XANA). The rest of the time, they're either comic relief or unexpected sources of help.
Danger Mouse has Baron Silas Greenback, his pet caterpillar Nero, and his henchman Stiletto Mafioso.
Donkey Kong Country has Klump and Krusha, with King K. Rool as the higher-up. Also, Captain Skurvy, Kutlass and Green Kroc.
The Urpneys (Sgt. Blob, Frizz and Nug) in The Dreamstone are very Team Rocket-ish; being rather sympathetic, doomed to failure from the start, and tending to get an unnecessarily hard time from the good guys after they've been clearly beaten already (bar a few occasions). In later episodes, Urpgor sometimes joins them, albeit in an often rivalistic manner.
Disney's DuckTales has the Beagle Boys, often as not with archnemesis Flintheart Glomgold as The Man Behind the Man. Sometimes their mother, Ma Beagle, tends to be in charge.
Donbot and his two goons, Clamps and Joey Mousepad, are the entire Robot Mafia.
Mom's three sons, Walt, Larry and Igner, are another Terrible Trio. Though they're not completely incompetant, Mom treats them as if they are. Their original plan to get Fry's PIN number only worked because Fry was being... well, Fry.
From Teen Titans, the HIVE kids. Jinx is the leader, with Gizmo and Mammoth working with her. They're pretty dangerous on their own if they put their minds to it, but generally need a higher-up to scare them into that level of competence — Slade in their first appearance and Brother Blood later. Ultimately they strike out on their own (and add a few more to their team), but without someone to direct them, they're basically just super-powered delinquents. And then Jinx finally gets fed up with that and does a Heel–Face Turn.
The Monarch, Henchman 21, and Henchman 24, all of whom are bumbling and ineffective. Higher Up is The Sovereign, also known as David Bowie. Except for more recently, when the Monarch is showing increasing levels of competence and 21 and 24 have some lucky moments. Well, in the last minutes of the season three finale, 24's luck ultimately runs out....
Doctor Girlfriend, with Tim-Tom and Kevin, the Murderous Moppets. She's coolly competent; the boys tend to get a little over the top and beyond mission scope... Higher Up is also The Sovereign.
A heroic version is The Order of the Triad, led by Doctor Orpheus, with Jefferson Twilight and The Alchemist. Higher Up is The Master.
Icy, Darcy and Stormy from Winx Club become this after Season One.