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.
Kamen Rider Gaim: Duke, Sigurd and Marika are this during the show's Yggdrasill arc, but the focus then switches to the villainous Overlords Roshuo, Demushu and Redyue. When Demushu is destroyed, Mitsuzane sides with Redyue and becomes the third of the trio. Later, Kaito becomes the main villain after transforming into Lord Baron; and another Terrible Trio forms with him, Yoko and Zack, though Zack is biding his time until he can find a way to defeat Kaito.