Astérix: The three main pirates are comprised of the red bearded captain, the black mate in the crows' nest and an older crippled pirate who speaks Gratuitous Latin.
There's a group of fairly obscure Batman villains called the Terrible Trio (who, as far as can be told, weren't in mind when naming this trope). Made up of the Shark, the Fox, and the Vulture, the Terrible Trio is of extremely variable threat, and they don't show up very often because they're pretty mundane as Batman rogues go.
The DCAU-tie in comic The Batman Adventures and its successor series had another group, the Threatening Trio; Mastermind (the groups egotistical leader), Mr. Nice (a One-Man Army whose weakness is he can't help but be nice and helpful to people he's stealing from), and the Perfessor (who has an encyclopedic knowledge of most things).
The Beezer used to have a set of crooks called The Bad Lads, Boss (short, bossy), Knuck (big, dozy) and Fingers (tall, gangly).
A recent backup on the Incredible Hulk book gave us Gamma Corps Black. A team made of 3 Distaff Counterparts, of Hulk villains Abomination, Zzazz and Glob. Aberration, Axon and Morras respectively.
The Madballs comic book published by Star Comics (a defunct subsidiary of Marvel Comics) had two examples of a villainous trio.
The third issue introduced the Badballs (Smasher, Crasher, and Trasher), who were three bowling balls the comic's main villain Dr. Frankenbeans accidentally brought to life while trying to deliberately create his own Madballs to defeat the originals.
The fifth issue introduced the Super Madballs (Touchdown Terror, Goal Eater, and Foul Shot), who were also created by Frankenbeans to battle the original Madballs, but ended up siding with the original Madballs instead.
In the Mickey Mouse Comic Universe, Mickey Mouse sometimes faces Professors Ecks, Doublex, and Triplex, three simian mad scientists who tried to use a Hypno Ray on Mickey and his friend Horace Horsecollar in their first appearance. All three of them are rather sadistic, though Triplex tends to be the one who's in charge.
Marvel has the Spider-Man/Daredevil villains The Enforcers — Montana, Ox and Fancy Dan. Later joined by Hammer Harrison and Snake Marston.
Marvel also gave us the merc group B.A.D. Girls Inc. Three female villains that used to be part of the Serpent Society.
Wonder Woman dealt with a terrible trio during her days as a non-powered boutique owner in the 1960s, the Creepy Crossdresser (or maybe, by implication, Psycho Lesbian) group known as THEM! Led by Top Hat along with Pinto and Moose Mama, they started harassing Diana when she began sheltering a young woman they had been keeping as a slave. THEM were stopped by the combining efforts of Tony Petrucci, a young man living in the same neighborhood, and Diana who had taken on Top Hat by herself after the other two and their brutish henchmen were taken care of. They were about as bizarre as Wonder Woman's villains could get, but only made one appearance.
Urbanus: Stef, Staf and Stylo, three criminals who differ in height.