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 Four Guardians from the Mega Man Zero games, who each lead a specific section of the Neo Arcadian army. 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).
The Hell Hounds in the Galaxy Angel gameverse, although they're much more serious (and creepy) in the manga.
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
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 squade. Of course, these being Metal Gear games, 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 Heel-Face 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.
Pokémon Yellow features Jessie and James from the anime series.
Umineko no Naku Koro ni 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 Siestas 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.
Touhou 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.
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.
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).