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.
iCarly: In some of their more Jerk Ass moments Carly, Freddie and Sam apply to this.
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.
Monty Python's Flying Circus. Did you expect to see The Spanish Inquisition here? Well, you shouldn't have. Nobody expects the Spanish Inquisition.
Bulk and Skull from the Power Rangersverse are Team Rocket minus one — they're a pair of comically stupid henchmen (one big and fat, one little and weasely) with no brainy leader. They later had a Heel-Face Turn. They acquired a leader later in the series, when they became cops, Lieutenant Stone. And later again, Professor Phenomenus.