In The Avengers, there's Loki, The Other, and Thanos. With Thanos as the leader, The Other as his servant, and Loki as a reluctant ally. The Other serves as communication between the other two, who are each considered antagonists of the film in their own way.
In Babes in Toyland, there's Barnaby, Gonzorgo, and Rodrigo. Barnaby hired Gonzorgo and Rodrigo to help him kill Tom, but the two mercenaries do a Heel-Face Turn, before Barnaby is presumably killed in a swordfight with Tom.
Batman & Robin has Mr. Freeze (brains), Poison Ivy (beauty), and Bane (muscle).
In Raiders of the Lost Ark, the main antagonists are Rene Belloq, Major Toht, and Colonel Dietrich. They get a pretty elaborate and iconic death scene when the open the Ark, each having his head destroyed in a different way.
In Spaceballs, you've got President Skroob, Dark Helmet, and Colonel Sandurz, who are similar to the above mentioned Terrible Trio in the Empire.
The three witches from Stardust: Lamia, Mormo, and Empusa.
In Star Wars, there's the three most prominent figures in the Trade Federation, Nute Gunray (leader), Rune Haako, and Daultay Dofine. Subverted in that Nute and Rune go to Naboo while Dofine stays aboard the Control Ship and is killed two movies before Nute and Rune).
Then you've got the three most prominent figures in the Empire itself, Emperor Palpatine, Darth Vader, and Governor Tarkin. Again, Tarkin is killed two movies before Palpatine and Darth Vader (and the latter's Heel-Face Turn), except it's Palpatine who is separated from the others in A New Hope).
Superman has Lex (brains), Eve (beauty) and Otis (ummm...)
Superman II has General Zod (brains), Ursa (beauty), and Non (muscle).
In The Texas Chainsaw Massacre 2, there's Leatherface, Chop Top, and Drayton (and Grandpa, but he doesn't do much). Like the boys from Cannibal Campout, they give off a definite Three Stooges vibe.
Likewise, their counterparts from the other side of the Iron Curtain. The Soviet comedic trio Nikulin, Vitsin & Morgunov play the Terrible Trio everywhere they appear. Notable in that the leader, Morgunov, has brains, brawn and assertiveness; one other guy is a brash hot-headed idiot and the other is smart but cowardly.