Sailor Moon had a set of these guys every season (in order of appearance: Shitennou, Ayakashi Sisters, Witches 5, Amazon Trio, Amazones Quartet, and Sailor Animamates). Many of these groups were made up of colour-coded evil counterparts of the Four Guardians (Ami, Rei, Makoto, and Minako). In the manga, the Witches 5 were even resurrected JUST to kill the Senshi they copied!
Futari wa Pretty Cure (including the numerous spin-offs) has a cadre of mid-level badguys every plot line, one of which usually ends up becoming The Dragon or are led by the dragon. This series has the Dark Five, later the Seeds of Darkness, and then the Four Guardians in the sequel.
Hugtto! Pretty Cure starts out with Charalit, Ruru, and Pappuru. Once they're out of the picture, it becomes Jelos, Dr. Traum, and Bishin. Poor Daigan ends up as a Bait-and-Switch Boss, and Listol rarely gets involved.
Kannazuki no Miko had the "Necks of Orochi", whose appearances parodied stock characters in anime. (As an aside, there were faceless mooks in the manga, but they never made an appearance in the anime.)
The Ginyu Force, as seen in the page image. They're the most powerful mercenaries in Frieza's galaxy-spanning army...and they introduce themselves with a well-rehearsed "Super Sentai" Stance, pick their opponents via RockPaperScissors, and discuss dinner plans with each other mid-battle. They do a pretty good job beating up the good guys - and Vegeta - before Goku comes along and tears them a new one.
Lampshaded and parodied in the Lord Slug Abridged movie; when Piccolo comes face-to-face with Slug's three top henchmen, he casually asks them what their gimmick is, noting that the last bunch he fought (in Christmas Tree of Might) were all misfit minions. His bored reaction as they list their gimmicks (the pretty one, the tough and stupid one, and the one with weird powers), makes it plain he's seen it all before. Then he comes across similar trio in Cooler Abridged, though the mooks didn't seem to get which one was which.
Sand Land: One of Akira Toriyama's more obscure works. It featured The Swimmers as a sort of nicer Ginyu Expy squad.
Trigun: The Gung-Ho Guns are the enemies of Vash the Stampede in led by Legato, though in a twist in the original manga, some actually have humanizing connections with him.
Bobobo-bo Bo-bobo features the various blocks and divisions of the Hair Hunters, which included in their ranks everything from robots to martial artists to Talking Animals to animated objects. Sometimes the objects aren't animated at all. There was an ordinary stick of gum in their ranks at some point. Ironicaly the gum actually won its fight. (By getting eaten, but it still counts.)
Grimmjow's Fracción who are completely loyal to him and prove to be extremely deadly to Hitsugaya's Advance Squad when they fight. Although the Shinigami do end up winning, victory is costly. It's even more costly for Grimmjow's group. Grimmjow is the only one who survives.
Harribel's Amazon Brigade are a trio of quirky females who appear to be barely able to stand each others presence. Nevertheless, they're incredibly dangerous and are capable of combining their power into a creature that manages to take out four lieutenants without effort and which needs to be defeated by Yamamoto-Genryuusai himself. In the final arc of the story, they're less villains and more aloof allies to the protagonists as they and the protagonists find themselves sharing an enemy.
Baraggan's Fracción are a strange mixture of beings, ranging from the dour and serious to downright kooky. None of them survive the conflict against the Shinigami, but they give the Shinigami a world of trouble before they're taken down.
It turns the Sternritter are this... not to Yhwach, but to Haschwalth. Established as a Bad Boss from the outset, Yhwach appears to command loyalty through fear whereas The Dragon Haschwalth appears to have the army's loyalty through respect and companionship. When the Sternritter feel Haschwalth has been snubbed by Yhwach in favour of Ishida, the personalities of the Sternritter begin to be explored. Quirky is is a mild description for some of them.
The Hyper-Zoanoid Five in Guyver. Of course, they barely fought the Guyver himself, and instead were targets for Aptom, who took down four out of five and even was able to get a sample of Zxtole's genetics.
The Homunculi in Fullmetal Alchemist beneath "Father" (in the manga) or Dante (in the first anime). Going a step below that, one of the Homunculi, Greed, has his very own mini-miniboss squad with his chimera henchmen (and henchwoman).
The Juppongatana in Rurouni Kenshin, almost all of whom have some underlying motive for helping Shishio and tragic backstories. The Six Comrades from later in the manga, however, are just Psychos For Hire.
The Genei Ryodan are comprised of 13 powerful thiefs, with each of them having a unique personality and abilities, but most of them share the same or have a similar background, which is the reason why they have a strong sense of companionship for each other. Their individual uniqueness form the 12-legged Spider, a metaphoric entity which the leader Chrollo Lucilfer identify as himself.
The Royal Guards who serve the Chimera Ant King. Each of them goes through drastic Character Development in a short amount of time, they all have their own ideas of loyalty and they show more and more of humanity in them (including the bad side of humanity).
Ashram's followers (Groder, Gaberra, Smeddy, Gilram, and Astar) from Record of Lodoss War. They were also Evil Counterparts to the heroes: Ashram for Parn, Groder for Slayn, Gaberra for Leylia, Smeddy and Gilram for Shiris and Orson, and Astar for Deedlit.
The Wolkenritter before them, in A's. Although the boss in this equation (Hayate) wasn't even aware of what was going on until the climax.
The Inherent Type Iris Units fill this role in Detonation, being more powerful than the Mass Production Types and having unique appearances and weapons. All of them go unnamed and they don't appear to have individual personalities.
Akatsuki tries to be this, giving each of its members a quirky personality, but few of them are considered expendable. Really they're more several pairs of Those Two Bad Guys (Deidara/Sasori, Kisame/Itachi and Kakuzu/Hidan) a Big Bad and his Dragon.
In a way, the resurrected Jinchuuriki and their Bijuus are this - the Bijuus have their own quirky personalities, their Jinchuurikis followed the Big Bad into the battlefield, and they perform a group HeelFace Turn once released from the Edo Tensei.
Pasder's Four Machine Kings (Polonaise, Primada, Pizza, Penchinon) from GaoGaiGar.
The members of the 31 Primevals who possess human bodies become one for a short time. Final has the 11 Mastersof Sol, though half of them are arguably a subversion. While set up with the fanfare of a quirky miniboss squad, they never reveal a personality, voice, or even a face. They are a shadow shaped like a miniboss squad.
In One Piece, almost every villain's named henchmen qualify as a quirky miniboss squad, with some Psycho Rangers thrown in. At first, they're always one miniboss to fight every crew member. As the crew has grown, this has been abandoned, and instead the minibosses have become so powerful than it may take two or three Strawhats just to beat one of them.
Gon Jem and his Shitennou in Metal Armor Dragonar. You don't get any quirkier in a Real Robot anime. Their weirdness does not keep them from being more than a match to the heroes in more than one occasion.
Samurai Deeper Kyo has several such groups. Perhaps most stunning is the fact that the protagonist and title character, Kyo himself has his own Quirky Miniboss Squad, the Shiseiten (translated as the Four Emperors in the american release). Also present are Sanada Yukimura's Sanada Ten and Nobunaga's Twelve God Shoguns. The primary villains of the series, the Mibu clan have several of squads of their own, the primary two being the Five Stars and the Four Elders. It gets even more complicated, however, when it is revealed that each of the four elders has his/her own Quirky Miniboss Squad, referred to as the Imperial Guards. Finally, the Crimson King has his own secret miniboss squad in the form of the Red Cross Knights, who serve as his secret assassins.
In a similar case to Kyo, Dark Schneider of Bastard!! is also a protagonist with his own Quirky Miniboss Squad (The Four Riders of Havoc). In addition said minibosses have their own minibosses (Especially Kal Su, who commands 13 Generals with their own quirks). And there's also the various high ranking Angels and Demons.
Berserk has two: The Bakiraka from the Golden Age arc, Proud Warrior Race Guys who are ordered to stop the heroes and the group of deformed torturers from the Albion arc, who are Improbable Weapon Users who receive demonic powers and are completely devoted to Mozgus, the Big Bad of that arc. The Bakiraka are killed by Guts and co while Guts completely defeats the torturers by himself.
Actually around chapter 340 or so, it's revealed that Nijima somehow got Loki to gather info for him, so it's currently 6 out of 8 fists now. And the jury's still out on whether Odin is still entirely loyal to his master.
Then, after the Ragnarok arc, we have Yami and YOMI, which both have Quirky Miniboss Squads. Yami has a leading group called "One Shadow Nine Fists", where "Shadow One" is The FacelessBig Bad and the "nine fists" are his Quirky Miniboss Squad. The organization of Yami's disciples, YOMI, also has its own Quirky Miniboss Squad which consists of those who are the disciples of "One Shadow Nine Fists".
Rave Master was chock full of these. Odds are if a main baddie is introduced, his squad wasn't too far behind.
Fairy Tail has several Quirky Mid-Boss Squads. The Paradise Tower arc pulls a bait and switch which introduces one squad of baddies who are easily trounced — but then brings out a much more serious bunch.
Later we're given the Raijinshu (Laxus's team) and the Seven Kin of Purgatory from Grimmore Heart. Element Four of Phantom Lord would also qualify.
Karacke, Rayule, Byard and Kageyama from Eisenwald under Erigor in the "Lullaby" arc.
Yuuka, Toby and Sherry from Lamia Scale under Lyon in the "Galuna Island" arc.
Element Four (Juvia, Totomaru, Sol and Aria) under Jose Porla in the "Phantom Lord" arc.
Firstly Erza's childhood friends (Wally, Millianna, Simon and Shou), then Trinity Raven (Fukurou, Ikaruga and Vivaldus) under Jellal in the "Tower of Heaven" arc.
The aforementioned Raijinshu (Evergreen, Bickslow and Frred) under Laxus in the "Fighting Festival" arc.
Oracion Seis except for their leader Brain/Zero (Angel, Racer, Hoteye, Midnight, Cobra and Klodoa) in the "Nirvana" arc.
The Royal Army (Pantherlily, Knightwalker, Hughes, Sugarboy and Byro) under King Faust in the "Edolas" arc.
The Seven Kin of Purgatory (Ultear, Zancrow, Kain, Azuma, Rustyrose, Meredy and Zoldeo) along with Deputy Commander Blunote under Hades in the "S-Class Trial" arc.
The Zentopia Church's Legion Corps (Bryo, Hughes, Sugarboy, Coco, Dan, Samuel and Guttman) under Lapointe and later the return of Oracion Seis (Racer, Angel, Cobra, Jackpot/Klodoa, Reaper/Erigor and Imitatia/Michelle) under Brain II/Midnight in the (now considered canon) anime "Keys to the Starry Heaven" arc.
All the other guilds' teams against Fairy Tail, most notably Sabertooth (Sting, Rogue, Rufus, Orga and Minerva) under Jiemma and Raven Tail (Alexei, Obra, Flare, Kurohebi and Nalpudding) under Ivan/Alexei, in the "Grand Magic Games" arc.
The Hungry Wolf Knights (Kama, Knepper, Uosuke, Cosmos & Kamika) from later in the same arc.
The Nine Demon Gates of Tartaros (Kyouka, Silver, Jackal, Tempester, Franmalth, Torafuzar, Ezel, Seilah, Keyes) under Mard Geer in the "Tartaros" arc
Jerome, Briar, Mary, Gomon, D-6 and Able from Avatar under Alok in the "Avatar" arc.
Shaman King's Lily Five team (but only in the anime), though they turned out to be good guys. There were also Hao's minions (who appear both in the anime and the manga). Despite having such members as a mariachi and a football player, they were all legitimately dangerous, as well as having a larger role in the manga. It ends up being quite surprising when members who were closer to mook status turn out to have been Hero Killers who had been holding back (in the manga, again). Especially the mariachi.
Innocent Venus has the Phantom unit, complete with a knife-licker and a Chinese man who kills people with rather sharp tarot cards.
The Four Chief Vassals of the King organization in Fist of the North Star, which consist of Spade, Diamond, Club, and Heart. Heart serves as The Dragon, being the only member of the group who provides a seemingly genuine threat to Kenshiro's martial art skills.
Mahou Sensei Negima! has Fate's group of partners, who start popping up in the Magic World. Unfortunately for them, they have a rather nasty habit of running into Jack Rakan.
Athrun, Yzak, Dearka and Nicol in Mobile Suit Gundam SEED. Although if they are on the good or bad side is a matter of perception. One ends up dying, and two join up with the 'good guys'.
The Big Five in the Virtual World arc. Each of them has his own backstory and they all have different personalities, decks and playstyles. While they are middle-aged or old men, they are often presented as their Deck Masters, which gives them visual distinction from each other.
And also the three Swordsmen from the Doma arc who all act as Foils and rivals to the three main wielder of the Dragon cards.
Yu-Gi-Oh!: Capsule Monsters has the five dragons of the fifth trial, who act as evil counterparts to the heroes. The final trial has Alexander and his vassals, who also correspond to the heroes.
Eyeshield 21 had this in the form of the Cyborgs and the Scorpions. Shinryuuji also had its own within their team who were shout outs to Journey of the West.
This trope was also deconstructed with the Chameleons and the Guts, as both quirky teams trained incredibly hard only to be curb stomped early in the tournament.
Dragon Ball used this trope a bit in its early days, but the Ginyu Force was the last obvious demonstration of it. However, it has been used quite a bit in the non-canon movies, to the point where Team Four Star lampoons it with classifications "Pretty One", "Stupid One", and "One with the Weird Powers".
Kill la Kill has the Elite Four, an ensemble of Satsuki's top lieutenants. Due to having well-fleshed backgrounds and undergoing constant development in terms of both powers and character, they are also considered somewhat of a Spotlight-Stealing Squad.
Spoofed in the Battlefield Trip episodes, where the Kyoto defenders pose themselves as this but end up defeated in a matter of seconds.
Ping Pong: Despite the team's skill, all of Kaiō Academy, excluding Kazuma and Sakuma prior to the latter's departure.
In Endride, the Truculent, start out as the main opponents of the Ignauts up until Babylon, when Louise defects properly and Ibelda slaughters their other teammates. They're all greatly different in appearance and have very different ideas about how to follow orders.
In Brave10, the Ishikawa gang take this place against the Braves in volume 4.
The "hounds" in Moribito: Guardian of the Spirit, who hound Balsa and Chagum's steps for most of the story and serve as the main physical threat from the Emperor's Court. Ultimately, as the story ends up with all human characters on the same side, they help Balsa defend Chagum in the climax and help shoot down the Emperor's plan to have Balsa assassinated.
Kuroko no Basuke: Each of the five members from the Generation of Miracles serve as a boss Seirin has to defeat. The four (and in one case, five) teammates of the respective GoM player can be viewed as this, since they are rather quirky and important enough to qualify as a miniboss squad, and generally, it's not uncommon that individual players are obstacles by themselves. However, while there's usually one player who is developed enough to serve as the The Ace's partner/best buddy, there tends to be at least one player who is rather the Generic Guy or Flat Character and doesn't stand out as much as the others. However, the team that fits this trope the most would definitively be Rakuzan, the final team Seirin has to face in the Winter Cup. All four players are quirkier than most other characters, have special skills that the other teams commonly lack, and each of them has enough interaction with individual Seirin players that would make them sort-of-rivals. The fact that three of them are "members" of the Five Uncrowned Kings makes Rakuzan even more threatening and quirkiernote Like the Generation of Miracles, the Five Uncrowned Kings used to be aces, and each of them had their own special skill and very eccentric personalities..