The List of Super Villain Teams

[Randy Jackson]

This is pretty short right now,  but I'm sure it will get significantly longer.  Anyway,  this is off the top of my head. 

To be eligible,  at least one team member must possess a super power or a scientific device used regularly that simulates one:

Here's the list:

Alliance of Evil

Ani-men

Anti-Fly League (The Fly)
Anti-Justice League

Awesome Foursome

Axis Amerika

Band of the Bland

Battle Axis (Invaders)

Brotherhood of Dada
Brotherhood of Evil
Brotherhood of Evil Mutants

Cadre
Chessmen(Astro City)

Circus of Crime

Crime Champions
Crime Syndicate Of America

Death Throes

Death Squad (Iron Man)

Electro and his Emissaries of Evil

Evil Eight (Dial H For Hero)

Factor 3
Fatal Five

Forgotten Villains

Frightful Four

Fearsome Five

Gang (Supergirl)
Ginyu Force

Grapplers (MTIO)

Headmen

Helix (Infinity,  Inc.) 
Hellfire Club Inner Circle

HURRICANE (Inferior 5)

Factor 3
Injustice Gang of the World
Injustice Society

Intelligencia (Marvel)

Lawless League

League of Challenger-Haters (Challengers of the Unknown)

League of Evil Inhumans

League of Super-Assassins
Legion of Super-Rejects
League of Villains
Legion of Doom
Legion of Supervillains

Legion of the Weird

Lethal Legion

Madmen

Masters of Disaster
Meta Liberation Army

Monster Association

Monster Society Of Evil

Mutant Force (Captain America)

New Enforcers

Nuclear Family

Omega Flight
Paranormal Liberation Front
Pyramid(Astro City)

Recombatants

Renegades (Freedom Fighters) 
Royal Flush Gang

Salem's 7 (Fantastic Four)

Serpent Squad/Society
Sinister Six
Sinister Society of Super Villains

Squadron Sinister
Super-Axis

Superman Revenge Squad (from the comics and animated series)

Tauros Gang
Team Carnivore(Astro City)
Team Rocket

Terrible Five

Terrible Trio (Batman)

Terrible Trio (Marvel) 

U-Foes
Unholy Alliance(Astro City)

United Underworld (BATMAN the Movie)

Wrecking Crew

Zemo and his Masters of Evil
Zodiac

[Dave Palmer]

Ani-Men

[Dave Palmer]

League of Evil Inhumans

[Dave Palmer]

[Dave Palmer]

[Dave Palmer]

The Eliminators

[Dave Palmer]

[Dave Palmer]

[Randy Jackson]

Added the following:

Ani-men
Death Throes
Electro and his Emissaries of Evil
League of Evil Inhumans
Legion of the Weird
Lethal Legion
Squadron Sinister
Zemo and his Masters of Evil

I need the actual name of the group to add it. 

[Philip Portelli]

From the Legion, there's

The League of Super-Assassins

The Legion of Super-Rejects

The Tauros Gang

From Justice League, there's 

The Anti-Justice League

The Crime Champions

From Spider-Man, 

The Sinister Syndicate

Plus:

The Renegades (Freedom Fighters)

Terrible Trio (Batman)

United Underground (BATMAN the Movie)

League of Challenger-Haters (Challengers of the Unknown)

Anti-Fly League (The Fly)

Superman Revenge Squad (from the comics and animated series)

[Philip Portelli]

The original X-Men fought Factor 3

X-Factor fought the Alliance of Evil

The New Mutants fought the Hellions.

Howard the Duck & the Defenders fought the Band of the Bland.

[Randy Jackson]

Added:

Alliance of Evil
Anti-Fly League (The Fly)
Anti-Justice League
Band of the Bland
Crime Champions
Factor 3
Hellions
League of Challenger-Haters (Challengers of the Unknown)
League of Super-Assassins
Legion of Super-Rejects
Renegades (Freedom Fighters
Superman Revenge Squad (from the comics and animated series)
Tauros Gang
Terrible Trio (Batman)
United Underground (BATMAN the Movie)

[Rob Staeger (Grodd Mod)]

From the first JLA Detroit story, there's the Cadre: