The Magnavore trio from Beetleborgs, consisting of Noxic, Jara and Typhus, are this in the first season of the show. Jara usually acts as the leader, Noxic, despite not being very smart, has shades of being an Evil Genius, while Typhus is pretty much The Brute. They serve Vexor as their higher up. Their successors of the second season, the Crustaceans, subvert this trope. While there are three of them, they don't necessarily operate as a trio.
Warren, Andrew, and Jonathan were amusing, ineffectual, wannabe-bad-guys... for a time. Andrew and Jonathan were in it more out of a craving for acceptance and the desire to fulfill their comic-book fantasies, and each of them eventually did a Heel–Face Turn (Andrew under duress, Jonathan of his own accord). Warren, however, was genuinely evil and had the makings of a real supervillain... but his budding career was cut short when Willow flayed him alive for killing Tara.
"Lessons", the premier of Season Seven, had a trio of malevolent ghosts (simply credited as Dead Girl, Dead Nerd, and Dead Janitor) haunting the rebuilt Sunnydale High.
And in Angel, there's Lindsey McDonald, Lee Mercer, and Lilah Morgan, the most prominent members of Wolfram & Hart to be seen in Season 1 (aside from their supervisor Holland).
Speaking of Wolfram & Hart, it is implied that there are three Senior Partners leading the law firm, although it goes down to two in Season 2 the one time a Senior Partner appears onscreen.
The Stillman Sisters from the Charmed episode "The Power of Three Blondes"; they also qualify as a collective Evil Counterpart to the Power Trio of protagonists. All three of them are trying to steal the Halliwell sisters' powers and prove that they're more than just a trio of blonde bimbos, and they come oh-so-close to succeeding at both. Mabel, the oldest sister, is clearly the leader and the most serious about the whole thing.
The Three Shogun from Chou Sei Kantai Sazer X are this during the first arc of the show. Fire Shogun Blaird is the brawny one, Wind Shogun Cyclead the brainy one and the bossy one is Water Shogun Aqual. These three villains spend almost as much time bickering with each other as they are fighting the heroes. After their boss, Captain Barder, is revealed to be a robot, the trio falls apart, as Blaird leaves to contemplate the purpose of their mission, starting his Heel–Face Turn. When the trio does reunite, all of them performed a Heel–Face Turn, forming another Power Trio to fight alongside the heroes.