In Advance Wars games from Black Hole Rising and onwards, the Big Bad of the evil faction usually has one of these. Black Hole Rising has Sturm employing Flak, Lash, Adder and Hawke (with Hawke being The Dragon) and Dual Strike has Von Bolt employing Jugger, Koal and Kindle, with Lash and Hawke returning from the former game (Kindle is The Dragon this time around). And they are very quirky. In Days of Ruin/Dark Conflict there are two 'evil' sides and each of them are too small to truly count one of these as part of their number.
Ape Escape: The Freaky Monkey Five fits this to a tee: Blue Monkey, the unicycle-riding rebel; Yellow Monkey, the flamboyant sumo wrestler; Pink Monkey, the psychokinetic diva; White Monkey, the eccentric old mech maker; and Red Monkey, the brawny and flatulent leader.
Brave Fencer Musashi had the Leader's Force, consisting of Ben, Ed, and Topo. They constantly fought amidst themselves over who was the leader of the three.
Mad Midget Five is a team of 5 midget Power Rangers with themes based around the suits of cards, led by Joker. Unlike most other Quirky Miniboss Squads, they are actually quite tough like all the other bosses in that game.
God Hand also has the Three Evil Stooges, who took Gene's arm in the game's backstory.
The Dark Knights in Tactics Ogre. Despite that most of them really aren't that quirky, some like Barbas do have a tendency to show off how powerful their discovery of a "gun" is only to shoot one of their own men.
Final Fantasy IV: Sandy, Cindy and Mindy (Japanese: Dog, Mag and Rag), the Magus Sisters.
The Turks, a subdivision of the Shinra corporation, from Final Fantasy VII are a classic example.
In Final Fantasy VIII Raijin and Fujin, Seifer's two sidekicks with their funny speech patterns. Raijin ends every sentence with "ya know?", (including a moment of silence in the beginning of the game). Fujin uses one to two word phrases, and speaks in ALL CAPS. It's a plot point when, near the end of the third disk, Fujin speaks normally and asks you to bring the Seifer they know back.
The first two games had the Four Guardians, who each lead a specific section of the Neo Arcadian military. Harpuia leads the airborne division, Fefnir the ground troops, Leviathan the navy, and Phantom the stealth units and intelligence division. And they have expies in the four enemy MegaMen in the Sequel Series, Mega Man ZX (specifically, Advent). Unfortunately, by Zero 3 Phantom is dead and the remaining three find themselves stripped of their positions to make way for...
Weil's Numbers are the new military commanders in Zero 3 after Dr. Weil convinces Copy-X Mk. II to make him the new head of military operations. Noticeably, the Numbers were formerly the Eight Gentle Judges of Neo Arcadia, tasked with overseeing the laws of the city-state, before Weil made them all Brainwashed and Crazy and recruited them as his muscle.
In Zero 4, with Dr. Weil having taken over Neo Arcadia but losing both Omega and the Numbers by the end of 3 at Zero's hands and saber, he creates a new squad out of the Einherjar Eight Warriors led by Commander Craft, tasked with destroying Area Zero or at bare minimum, run distraction on Zero and the Resistance while he prepares Operation Ragnarok.
The Hell Hounds in the Galaxy Angel gameverse, although they're much more serious (and creepy) in the manga.
Magus' three "sidekicks" from Chrono Trigger: Ozzie, Slash, and Flea. Although Slash on his own is a running candidate for That One Boss the first time he's fought on his own, all of the trio's other appearance, individually or as a group, are not that hard. The two times Ozzie is fought alone, he just puts up a barrier and sits there until you figure out that you need to hit a switch behind him to beat him. Even their optional three-on-three boss encounter during the endgame side quests is easy compared to some of the other sidequest bosses.
Solt and Peppor from Chrono Cross. They appear at seemingly arbitrary points in the game, their appearances never move the plot forward, and they are so much weaker then the party during their later appearance that they begin to border on Ineffectual Sympathetic Villain status. That is until they call out their superior, Karsh, for the murder of Dario, and actually do get serious. This fight is completely optional, and they actually make credible threats in this go around.
During one (and only one) appearance in one of the many alternate story paths, they even have a third member- the hulking Ketchop, who to their dismay started using Solt and Peppor as weapons.
And then there's the Dragoon Devas, consisting of the aforementioned Karsch (with betrayal issues), Marcy (get your ass kicked by a 9-year-old Tyke Bomb), and Zoah (hulking, loud giant behind a mask). They at least join the party after a while.
The Minions of Saruin from Romancing SaGa. However they are not as quirky or bumbling like other minions in other games, since everything bad that has happened was because of their actions. You actually have to end up fighting all 3 in the final dungeon in the original SNES Version, but in the PS2 Remake you only had to fight one, however if you defeated all 3 in the final dungeon, then you have the same results as the SNES version
The Super Smash Bros. series always has a mob of character models before you face the final boss; the first game has the Fighting Polygon Team, Melee has the Fighting Wire Frames, Brawl has the Fighting Alloy Team, and the fourth game has the Fighting Mii Team.
Star Fox 64 has Star Wolf, a group of four pilots in ships that were identical to your team's. They come back later with Amusing Injuries and Electronic Eyes piloting improved ships on the hard route (even if you didn't take the path where you fight them normally first). They also appear in the pretty much same way in Assault and Command, but with two of the original members gone and only one replacement, and with a dose of Defeat Means Friendship and Enemy Mine.
Final Fantasy IX had court jesters Zorn and Thorn, who later turned out to be less "quirky" and more freaky. It also had the Black Waltz, a trio of elite Black Mages.
Most of the Metal Gear games have their own distinctive boss squad. However, they are portrayed relatively realistically, at least compared to other examples, replacing "quirky" with "homicidal", "batshit insane" and "nightmarish".
The Fire Emblem series in general has used this trope in every game since Binding Blade, possibly earlier. Most of these squads have three or four members; of those, one is often recruitable, and one is often fought either in the endgame or the chapter right before it.
The four bosses from the Duelhorn storyline in Final Fantasy Tactics A2 appear to be pretty much this, but you never fight them together and they actually overthrow their superiors (that you never meet) at the end.
E-101 Beta, E-103 Delta, E-104 Epsilon and E-105 Zeta from Sonic Adventure (with a remodeled Beta as The Dragon). E-102 "Gamma" has a HeelFace Turn and decides to rebel against his robot brothers.
Sonic Lost World has the Deadly Six. However, about a third of the way into the game, they become more of a Quirky Big Bad Squad.
The Hard-Boiled Heavies of Sonic Mania; a team of Eggrobos that were enhanced by the power of the Phantom Ruby and serve as bosses throughout the game in addition to Eggman himself. However during the True Final Boss, their leader, Heavy King, has had enough of Eggman's blundering and goes into business for himself, turning the final boss into a Dual Boss with Eggman and Heavy King fighting Super Sonic and to keep the Phantom Ruby from one another.
This game only has three Cipher Admins before reaching the Big Bad's lair: Lovrina, whose Valley Girl speech pattern disguises the fact that she's the Mad Scientist, and who mixes Ein and Venus's strategies; Large Ham Snattle, who favors Explosions; and The Brute Gorigan, who follows Dakim's example with an Earthquake team.
We also have the Hexagon Brothers, six grunts that are just a step above Mooks and color-coded by the Type of Pokémon they use: red Resix uses Fire, blue Blusix uses Water, brown Browsix uses Groundnote Or rather, his Shadow Pokémon is Ground; he specializes more in Normal-Types, yellow Yellosix uses Electric, purple Purpsix uses Poison, and green Greesix uses Grass.
Umineko: When They Cry has the Seven Sisters of Purgatory, a team of red-eyedMs Fanservices with Names to Run Away from Really Fast, each representing one of the Seven Deadly Sins. Although they commit numerous murders, they're also just playful sisters that later are summoned by the protagonist's sister, Ange, as her only remaining friends. One of them lets the protagonist chase her around for stealing his breakfast, so "quirky" is a good word for it. They also like to smother Maria's stuffed lion-turned Sakutaro. Later on the Chiesters appear. And then the Eiserne Jungfrau show up.
Wild ARMs 1 has the Quarter Knights (Belselk/Berserk, Alhazad, Lady Harken, and Zeikfried/Siegfried), who play with this trope a bit. Belselk is killed off early on in the game, only to be replaced by Boomerang. Also, when the Big Bad that they are trying to revive ends up wanting to destroy the world rather than conquer it, they betray her. Even after Mother revives herself and possesses Zeikfried, they still remain a prominent threat, rather than becoming a Goldfish Poop Gang. In fact, Zeikfried defies all odds and ends up surviving Mother's possession to become the final boss.
City of Heroes has several, including Lord Recluse and his lackeys, and also their lackeys, who being supervillains have plenty of natural quirks.
Touhou Project tends to have single bosses rather than squads, but the Prismriver Sisters fall into this trope. Touhou fanworks also have "Team 9" led by Cirno, who are always getting into some manner of mischief or another.
Cannon Dancer has the Teki ("Barbarians"), a group of three elite warriors. Kirin, their former ally, battles each of them throughout the game (the order being determined by a pair of branching paths), then all at once in the final stage in a formation they call, "Die Rudeltaktik."
Ys IV(both versions) has the Clan of Darkness, V has the three mages, and VI has the Fairies, who fight alongside Ernst in the penultimate battle.
The Mega Man Legends series has two sets. The first game introduced the Bonne family (Teisel, Tron, and their baby brother Bon) and their Servbots, and its direct sequel added a pair of Sky Pirates named Bola and Klaymoor.
The MARDEK series has the World's Saviours, a second group of adventurers.
Mega Man Battle Network 6 had Yuika's LoveliesThe Justice ClubThe Cloudy Bombers the three minions who defected from WWW and can't agree on a new team name. The Darkloids (BlizzardMan, ShadeMan, CloudMan, and CosmoMan) from Battle Network 5 also qualify, though each of them works alone most of the time (and they didn't really provide any comic relief).
Yu-Gi-Oh! Reshef of Destruction has the elite Neo Ghouls: Rare Hunter, Arkana, Strings, and Lumis and Umbra. It also has Pegasus's lackeys: Panik, Puppeteer of Doom, Mimic of Doom, the brothers Para and Dox, the illusions of Espa Roba, Bonz, Rex, Weevil, Mako and Mai, and the brainwashed Mokuba.
In Yu-Gi-Oh! Monster Capsule GB, Mokuba, Weevil, Rex, and Mai are Kaiba's four Dark Masters and control the RPG Worlds housing one of Yugi's friends.
Neo Contra has the titular group of the same name. Aside from their leader Master Contra, there's the Elite Four, which consists of Guerrilla Contra, Plant Contra, Pheromone Contra who is actually Lucia from Shattered Soldier, and Animal Contra.
The second Digital Devil Saga game has the Tribhvana, the Karma Society's elite guard. They're a trio consisting of the manic Air, the aggressive Heaven, and the stoic Earth. You fight them three times, though they're a lot less quirky the third time when Earth eats the other two alive to gain more power.
World of Warcraft uses this a LOT. This is largely because Big Bads in this game usually need to build armies, so they need at least a few boss-level minions. Usually each member of the squad commands an order or some other kind of faction within the Big Bad's evil army. Either that or they are at least working on separate projects because the Big Bad's plans tend to be very large scale. There are at least four examples, but the best known is the Shadow Council: composed of Gul'dan, Lord Banehollow, Cho'gall, Nagaz, Jergosh the Invoker, and Taragaman the Hungerer. They are certainly quirky, in that they have a wide diversity of abilities and are from several different cultures. They are the behind-the-scenes leaders of the First Horde in the original Warcraft games (through Warchief Blackhand), and after a slight change in membership appear in World of Warcraft ...as agents of the Burning Legion.
The various antagonistic bomber teams from the Bomberman series starting with the Five Dastardly Bombers from Super Bomberman 2.
Exit Fate has two in one game: the Caretakers and the Commandos. The Caretakers get one group battle before the group fractures in their second encounter with the party (thanks to Boris' death and Orlando's HeelFace Turn). The Commandos appear more often, but after defecting to Almenga they suddenly aren't so quirky.
The Reborns from Iconoclasts are a group of three bosses who form a Fighter, Mage, Thief trio and serve as the sub-bosses for the One Concern East area of the game.
Undertale has the Snowdin Canine Unit, a group of guard dogs who are dressed for war, but aren't all that sharp in the upstairs department.
No Straight Roads has every artist that officially represents it, especially 1010, the local boy band comprised of five color-coded members and their manager. They're still just as challenging as any other boss fight.