The Strike Team on The Shield follow this mold, as far as the characters Shane Vendrell, Ronnie Gardocki, and Curtis "Lem" Lemansky serving as a quirky miniboss team for Vic Mackey. Indeed, by the end of the series, Shane murders Lem while Ronnie and Shane end up hating each other, right down to Ronnie keeping Vic from calling off a scheme to kill Shane.
Most Super Sentai and Power Rangers seasons feature a Quirky Miniboss Team for the big bad, who often (depending on the whims of the writers) either die, reform, disappear off the face of the Earth, or manage to escape justice by the end of the season.
Gosei Sentai Dairanger has the Three Idiot Gorma, who are not good at the whole acting evil thing and are more into thinking about new sports games to play with the Dairangers.
Zyuden Sentai Kyoryuger has the Zetsumates note (pun on zetsumetsu, which is Japanse for extinction) . This trio of monsters managed to kill off the dinosaurs in prehistoric times, but are rather comedic villains during present time. They even acted as an evil parody of a ranger team, pissing off the real rangers.
In WWE, the Spirit Squad acted as a Quirky Miniboss Squad in the Shawn Michaels vs. Vince McMahon feud, and D-generation X vs. McMahon Family feud.
There was also Shane McMahon's buddies, the Mean Street Posse.
This is pretty much what The Nexus was any time Wade Barrett wasn't there to lead them
Same thing now that CM Punk is in charge of The Nexus and Wade Barrett's leading the Corre.
H.R. Pufnstuf: Witchiepoo's henchmen: Orson Vulture, Seymour Spider, and Stupid Bat
In Buffy the Vampire Slayer, Glory had a small following of grovelling servants who, for the most part, served no purpose other than to elevate her ego. On the one occasson they did try to be constructive, they were beaten down by Buffy's superior man-handling skills.
There's also The Troika. Though not members of any larger dominant unit, they form their own Quirky Miniboss Squad, who's sole purpose is to enslave Buffy and force her into a life of servitude. However, their 'devilish' schemes are constantly thwarted, ending more often than not in pain and humiliation. Being geeks, they are probably consciously emulating this trope.
In the French Canadian Tv series "Les rescapés (The survivors)", the followers of the evil priest Chabanel serve as a quirky miniboss squad, each with their own distinctive personality quirk. Viateur is extremely violent and Trigger Happy, Jean-Luc is cowardly and keeps going through the Heel-Face Revolving Door, and Marguerite is the most mysterious, but also the most competent. When Viateur died, his role was taken over by a previously namelessmonk.