Afterlife Battlefront (Angel Beats!)
Planet Trade Organization [Frieza's Army] (Dragon Ball Z)
White Council (The Dresden Files)
Robot Masters (Mega Man)
Maverick Hunters (Mega Man X)
Autobots (Transformers)
Decepticons (Transformers)
Justice League (DC Comics)
Ginyu Force (Dragon Ball Z)
The Returners (FFVI)
Avalanche (Final Fantasy VII)
Death Eaters (Harry Potter)
Organization XIII (Kingdom Hearts)
Koopa Troop (Mario Bros)
SOS Brigade (Melancholy of Haruhi Suzumiya)
FOXHOUND (Metal Gear Solid)
The Cobras (Metal Gear Solid 3)
SEES (Persona 3)
Power Rangers (Power Rangers)
nWo (Pro Wrestling)
The Corporation (Pro Wrestling)
Liberation Army (Suikoden)
Royalist Army (Suikoden V)
Jedi Council (Star Wars)
The Empire (Star Wars)
Shadaloo (Street Fighter)
Cyberdyne (Terminator)
Brotherhood of Mutants (X-Men)
X-Men (X-Men)
Team Urameshi (Yu Yu Hakusho) [If they count]
We need to get something from Gundam in this, but I'm not sure what to bother nominating. I'll second anything that gets started.
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You know what they say: If you can't beat them, join them. If you can't join them, burn their house to the ground!