I'd like to offer a few suggestions (those most in need of support are bold). Though obviously I'm sure you'll have your own favorites.
Mad Hatter's Tea Party.
Order of the Phoenix
Dumbledore's Army
The Heavenly Host (Apocryphal Biblical)
The Nine Rings of Hell (Apocryphal Biblical)
The Lost Boys (Peter Pan)
The Midnight Crew
STARS
The A-Team
Charlie's Angels
MI-6 (The fake version we see in James Bond)
Quantum (New James Bond)
SPECTRE (SPecial Executive for Counter-intelligence, Terrorism, Revenge and Extortion) (The Original James Bonds)
The Returners (FF6)
Consumer Recreation Services (CRS) (The Game)
LexCorp (Superman)
Umbrella (Resident Evil)
Rainbow Rumpus Party Town (Homestuck)
Cyberdyne (Terminator)
The Breakfast Club (The Breakfast Club)
The Dead Poet's Society (The Dead Poet's Society)
ISIS (Archer)
The Xtacles (Frisky Dingo)
The City Watch (Discworld)
The Rebel Alliance (Star wars)
The Empire (Star Wars)
The Nazgul (LotR)
The Ministry of Silly Walks (Monty Python)
Knights of the Round Table (General)
The Shadow Proclamation (Doctor Who)
The Silence (Doctor Who)
Men of Low Moral Fiber (Monkey Island)
The Three Amigos! (The Three Amigos!) (These are the characters in a fictional film franchise within the film)
The three amigos (The Three Amigos!) (This is the 3 people who actually become a roving band of heroes)
The Forty Thieves
The Crazy 88 (Kill Bill)
The Deadly Viper Assassination Squad (Kill Bill)
The Trio of Outlaws (The Princess Bride)
The Zoo of Death (The Princess Bride)
The Brute Squad (The Princess Bride)
Whatever the society is called in The Lion King (The Lion King)
The Beast's Legion of Singing Furniture Servants (Beauty and the Beast)
The Cantina Band (Star Wars)
Jabba's Cronies (Star Wars)
The Church of Plasticism (General)
Urine Good Company (Urinetown)
The Urinetown Rebellion (Urinetown)
The Pirates (:Pirates of Penzance)
La Resistance (South Park)
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In the name of Seaworthiness