Evil GeniusChick - Princess Kycilia (she was the one to actually research and deploy Newtypes, instead of just using them for propaganda. Also the one to re-hire Char, which was smart but not terribly foresighted...)
The Dark Chick - NicolAmalfi: Probably the least capable pilot, Nicol makes up for it via technological advantages, including a cloaking device. Normally he'd be The Evil Genius, but on this team, his smarts make him stand out as much or more than his nice guy personality.
The Dragon and Team Dad - NeoRoanoke: Djibril's right-hand man, Neo leads the Phantom Pain strike team and keeps the Extended in line, while serving as the Earth Forces' best field commander and a capable mobile suit pilot to boot. He eventually Heel Face Turns.
The Evil Genius: Archduke Gorgon. On the surface he would seem The Brute, but in reality he was a manipulative, conniving, scheming, Magnificent Bastard prefered using his intelligence before his -considerable- physical strength- and provided The Big Bad with increasingly powerful weapons.
The Brute: Count Brocken. Although he is not so physically powerful like Gorgon, he commanded his own corps and would often rather using strength instead of cunning. He is an ex-Nazi officer, so he definitely liked getting his hands dirty.
The Dark Chick: Viscount Pygman. He was not a girl but he definitelystood out and he definitely was considered a freak. His skills, abilities and powers were also very different of his colleagues' ones.
Villain Secret Service - the other three Valkyries (Lee, Nobue and Jeanne by name). All three are convinced to Heel-Face Turn when Mashiro tells them that they have a bigger enemy to fight. Their boss vehemently refuses to turn, leaving her all alone on the side of bad.
The Evil Genius - Fortis (Seems to be the "brains" of the group and Curren's second in command of sorts when she's absent. Also has a calmer and more affable attitude than most of his comrades, save Curren).
The Evil Genius: Kidomaru (who looks like he fits the "less manically evil" trope until he's left alone with the heroes, then proceeds to get his sadistic nerd on.)
The Brute: Jirobo (a light subversion in that he's quite smart enough to couple his attacks with some serious emotional abuse. Also seems to have the most common sense of the group. Evil Counterpart to Choji)
The Big Bad: Deva Path. By far the strongest, and most destructive of the six; has the body of Nagato's best friend Yahiko, acts as the field leader, and is the last one standing, taking on Naruto's eight tails form mano-a-mano.
The Dragon: Animal Path I —> Animal Path II. Pain's first line of offense, and the one's he values the most after Deva and Naraka Paths. Have the most openly destructive powers after Deva, being capable taijutsu users and the most powerful Beastmasters yet witnessed in series. The original was able to fight Jiriya for some time on a fairly even keel, while the second wrecks half of Konoha with her Bond Creatures and briefly engages Naruto in a one-on-one fight.
One Piece has a number of these, generally introducing a new set for each new arc, although several sets are recurring enemies. Chronologically, the first example for both groups is the main members of the Buggy Pirates:
Dark Chick - Hatchan (Although he is Arlong's First Mate and Zoro's opponent for the Arc, usual qualificaitons for a Dragon, he is the resident "quirky" villain, and the only one to eventually get redeemed)
The Evil Genius - Wagnard (Spends most of his time down in the dungeon reading unholy scrpitures and summoning ancient demons.)
The Brute - Karla (Relies on raw magical force to obliterate her enemies, rather than tome or artifact-derived spells and incantations. Something of a Sixth Ranger Traitor.)
The Dark Chick - Pirotess (the Dark Elf. Ashram's evil, devoted, very hot and verystrong girlfriend. Like Deedlit, relies on elemental magic and familiars. Also, one of the few evil characters with any defensive abilities...)
Non-Action Big Bad - Sakyo, the owner of Team Toguro, and the mastermind of the Dark Tournament
Dragon-in-Chief - Toguro the Younger, the strongest member of Team Toguro, and the singular biggest threat in the entire Tournament. Fear of him forced Yusuke into the Tournament in the first place
The Evil Genius - Karasu, a bomber-demon on par or better then Kurama in the way of smarts. It took a transformation into the Demon Fox to outfox him
The Brute - Bui seems like a textbook case: heavy armor, Big Friggin' Axe, and a tendency to not speak. However it turns out that the axe is by no means his best weapon, he is quite the eloquent speaker when he wants, and the armor is actually designed to limit his dangerously strong battle aura
The Dark Chick - Toguro the Elder, clearly the most unhinged demon on the team, even moreso then the sadistic Karasu. Nearly immortal and capable of twisting his body into any number of truly grotesque mutations
Evil Genius - Pride/KingBradley. Deep-cover agent who masterminds the implementation of the plan, provides troops and battle strategies, and interferes with the heroes' efforts to undermine the Big Bad. Doubles as a second Dragon during the finale.
Miboshi an evil buddhist monk and demon summoner didn't get much screen time but was probably a second Evil Genius. Amiboshi is technically a team member but he first spies on then defects to the good guys - his power is musical human puppetry.
The Dragon: Guame ( He was Lordgenome's pet back when he was still a Spiral Warrior, essentually making him an Evil Counterpart to Boota, and Guame can take liberties with talking to Lordgenome that would get one of the other three generals killed where they stood)
The Dark Chick: Misty, becomes a Dark Signer under sympathetic circumstances, is redeemed before losing.
The Evil Genius: Carly, though she overlaps with Dark Chick too. Manipulates Jack's inner feelings and desires to try and provoke a Face-Heel Turn.
The Brute: Devack, uses an Ape deck, imprisoned Luna's Signer Dragon. When he's defeated he's replaced by Grieger, who duels more strategically but is just as brutal and powerful. The two of them are also physically large.
The Evil Genius: Antinomy, the group's chief manipulator who has all the best gadgets and uses a high-tech deck.
The Brute: Paradox, likely the most powerful next to Z-ONE (given that he can control time), focuses on bringing out powerful monsters as quickly as possible.
The Dark Chick: Sherry Leblanc. She stands out in that she is the only female, joined the group much later than the others (or would that be earlier?), and is unsure about Z-ONE's goal, having been coerced into helping.
The Dragon: Shiki. He's Creed's field commander, carries Creed's orders to the other Apostles of the Stars, is the most threatening after Creed himself, and must be defeated before Train can battle Creed.
The Brute: Maro. A sumo-wrestler who controls gravity. Not actually a member of the inner circle, he's obviously the highest ranking of the outsiders, and relays Shiki's orders to them.
While their efforts are generally unconjoined and seperate from each other, the employees of Easters innerwards workings can be seen like this until Nikaidou, of all people, makes a heel - face within episode 23.
Big Bad: Kazumu, until Gozen's existence is revealed within episode 22, although Kazumu still displays more traits of the trope (Aside from the fact that Gozen, for most of the series, never shows any portion of his body (Or his real voice.) towards any - one.) and commands the other operatives and the fact that he's (Albeit probably unintentionally.) partially responsible for Gozen's current condition any - way.
The Dragon: Kazumu towards Gozen, and perhaps Nikaidou towards Kazumu him - self (While not particularly loyal towards Kazumu, he seems the one most focused upon his "job", and is probably the most apparently "dedicated" towards it. (Ironically, he is the first to heel - face.) He also has a personal vendetta towards all of the Guardians, and, within fact, every being possible with a Heart's Egg: Jealousy due towards the loss of his own as a child, soon before it was about to hatch.)
The Evil Genius: While not exactly a genius, Nikaidou probably at first fits this role, at least more than the other workers: He devises each plan of his own to capture the Embryo, including, rather than capturing the original Embryo, simply making a new one instead. Still has evil methods, though. He can also build fully operational combat robots, as well as the machinery he uses occassionally for his plans, some - thing which stems from his child - hood dreams to be a robotics programmer. Later upon, Yukari probably takes more of this role, due towards her finding new ways and researching more technologies in order to amplify the corruption powers of Utau's voice. And the fact that Yuu just heel - faced.
The Dark Chick / The Brute: Utau, who shares the chickish trait of being captured prisoner... Only towards Easter's whims, not the Guardians. This is because the sole reason she works for them is due towards probably - violent threats towards her mother and, more importantly, Ikuto. And when she does find the Embryo, the only reason she'll take it is the desire towards wishing towards her and Ikuto's freedom. She's also the greatest offensive power the corporation have, which confirms her for the latter role, although she usually doesn't take pleasure for it, thus halting her from Brute position. Ikuto would also count, seeing that his Black Lynx Character Transformation form is probably upon par with Utau's Lunatic Charm Character Transformation (Although Dark Jewel may be another story, despite the time limit.) and that he is within partly the same situation, only with threats towards Utau and his mother (The same one as Ikuto's.) instead, but seeing as he's less likely to obey the smaller details of his orders and presented as far less helpless than Utau...
Friendly Enemy / Token Good Teammate / Enigmatic Minion: Ikuto, towards the point of being a main love interest. He screws around with the workers' (Especially Kazumu's.) plans and helps Amu and the other Guardians whenever he can afford towards, and constantly acts at least uncommunicatively towards any of the employee's aside from Utau, his sister. Hell, Yuu even spies on him at times to be safe. Also becomes somewhat of a Brute when he gets Brainwashed and Crazy later upon.
Co-Dragons: Rikiya Gaou and Hiromi Kisiragi, described as Hakushuu's Right Hand and Left Hand by Marco, Hiruma, and most commentators. Gaou breaks quarterbacks, runningbacks and linemen, while Kisiragi cripples recievers.
The Brute: Subverted. Marco clearly has former team ace Tengu slotted for this role, due to his status as their best linebacker, but Tengu pissed off Gaou (which never ends well) and Marco was forced to use himself and Gaou to fill the gap in the defence.
The Brute: Tatanka, perhaps the series crowning example of Dumb Muscle. He's tall, strong, a superb reciever, and a total dunce who's attempts at learning other languages have screwed up his ability to speak English.
The Dark Chick: Bud Walker, action movie star and wannabe cornerback. What exactly is he doing here?
In the Mai-HiME manga, the Searrs Foundation has this.
The Evil Genius: Riku Ousei, a complete sociopath with a keen intellect and an obsession with imagination, who is always cooking up new schemes to prove the superiority of his mind, in his own twisted way.
The Dark Chick: YurianneFaithful and JackSmith, both of which have a noticeable difference from the others - Yurianne is the only woman in the group, while Jack is a human-sized Arma with free will and feelings.
Dark Chick: Mamo, the only woman of the Selfish Trio. And Leva, the Camp Gay guy of the Selfish Duo.
Bigger Bad: Proto-Jikochuu. He corrupted King Trump and turned him into King Jikochuu, but he has little to do with the plot and only appears in the final episode, just to be killed by Cure Heart. And unlike the other Bigger Bads in this franchise, he's not really The Man Behind the Man.