This was done without looking at anyone elses nominations, so there are probably good ones that I missed, but anyway:
S.E.E.S (Persona 3)
Cruxis (Tales of Symphonia)
The God Generals (Tales of the Abyss, if they qualify)
The Order of the Phoenix (Harry Potter)
Dumbledore's Army (Sue me, I like Harry Potter)
The Al Bhed (Final Fantasy X)
Organization XIII (Kingdom Hearts)
The Fellowship of the Ring (Lord of the Rings, not sure if this one qualifies either)
The Reapers (The World Ends With You)
Fight Club/Project Mayhem (Fight Club)
This is all I can think of for now