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 seven spinoffs) 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.
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 from Dragon Ball Z, as seen in the page image. 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 has a quirky group of followers 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 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 followers 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 Stern Ritter 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 Stern Ritter feel Haschwalth has been snubbed by Yhwach in favour of Uryuu, the personalities of the Stern Ritter 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 back stories. The Six Comrades from later in the manga, however, are just Psychos For Hire.
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.
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 Heel–Face Turn once released from the Edo Tensei.
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-Moss 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 in the "Lullaby" arc.
Yuuka, Toby and Sherry from Lamia Scale in the "Galuna Island" arc.
Element Four (Juvia, Totomaru, Sol and Aria) in the "Phantom Lord" arc.
Firstly Erza's childhood friends (Wally, Millianna, Simon and Shou), then Trinity Raven (Fukurou, Ikaruga and Vivaldus) in the "Tower of Heaven" arc.
Raijinshu (Evergreen, Bickslow and Fried) in the "Fighting Festival" arc.
Oracion Seis except for their leader (Angel, Racer, Hoteye, Midnight and Cobra) in the "Nirvana" arc.
The Royal Army (Pantherlily, Knightwalker, Hughes, Sugarboy and Byro) in the "Edolas" arc.
The Seven Kin of Purgatory (Ultear, Zancrow, Kain, Azuma, Rustyrose, Meredy and Zoldeo) in the "S-Class Trial" arc.
The return of Oracion Seis 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) and Raven Tail (Alexei, Obra, Flare, Kurohebi and Nalpudding), in the "Grand Magic Games" arc.
The Hungry Wolf Knights (Kama, Knepper, Uosuke, Cosmos, and Kamika) from later in the same arc.
The Nine Demon Gates of Tartaros (Kyouka, Silver, Jackal, Tempester, Franmalth, Torafuzar, Ezel, Seilah, Keyes), in the "Tartaros" arc
Shaman King's Lily Five team, though they turned out to be good guys. There were also Hao's minions. Despite having such members as a mariachi and a football player, they were all legitimately dangerous. 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. 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'.
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".
Spoofed in the Battlefield Trip episodes, where the Kyoto defenders pose themselves as this but end up defeated in a matter of seconds.
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.
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.