I don't see why not. Here's the teams/orgs I thought of off the top of my head for this:

[center][b]Good[/b][/center]

Global Defense Agency – A global organization that secretly works with superhumans to protect the world.
GI Joe – A worldwide anti-terrorist organization.
Bureau of Paranormal Research and Defense – An organization dedicated to defending the world against paranormal threats.
Teenage Mutant Ninja Turtles – A group rumored to patrol the streets of New York.
MI6 – British intelligence agency. Has formed a team of extraordinary people to defend the country in times of need.
The Watcher’s Council – An ancient organization dedicated to rooting out evil on the planet along with serving and training the Vampire Slayer. The current slayer is teenager Buffy Summers.
The Autobots – The remnants of the Army of Cybertron, the Autobots now scour the universe for a new home while continuing their fight against the evil Decepticons.

[center][b]Evil[/b][/center]

Cobra Command – An eccentric band of international terrorists and super villains which use a snake/lizard motif
The Foot – An ancient ninja clan. Led by the mysterious Oroku Saki, they have come to New York to secure goals yet unkown.
The Decepticons – Villainous and traitorous Decepticons attempted to seize control of the planet Cybertron and the Cybertronian Empire. Their war with the Autobots ended up destroying their homeworld and scattering the Transformer people across the stars.
SPECTRE -- International terrorist organization who often clashes with James Bond.

I'm sure we'll have more to add to the list once we get going.