~Lets See so far~
Team Rocket (Leafgreen/Firered, Blue/Red/Yellow, Gold/Silver) - Trying to steal Pokemon from Trainers, the Leader created a Mewtwo from a Mew design. Took over Mt. Moon for some unknown reason?!? Captured an old dude in the Ghost tower. Took over A corp. building and set up an Illegal Gambling Pokemon game. Plus Cutting off Slowpokes tails in G/S! I can't remember G/S that much I think they did more!
Team Aqua and Team Magma (Ruby, Sapphire, and Emerald)
Releasing two Ancient pokemon one to try to make the Sea rise and one to try to make Land overtake the oceans. Aqua Stole a Submarine. Magma Tried to make and Volcano erupt with machines. Just two Teams obsessed with Water and Fire pokemon.
Team Galactic (Pearl/Diamond)
Has several locations in the game. Doing research and kidnapping people and some of there pokemon to do there dirty work. Atempting to bomb a town. Capturing Uxia, Mespirt, and Azelf and stealing thier chains. Trying to make a new world by setting free Daglia and Palkia. There Leader is really insane and talks to much!
Team Snagem (Pokemon Col. 3 for GCN)
Capture pokemon from trainers with a Snagem Machine, and make them Shadow, which can attack people. (Played half way thru the game, it as okay but a bit pointless with having to make Pokemon Unshadowy again and not being able to add them to my GBA games or trading back and forth.)
Cipher (Pokemon XD)
Making a Shadow Luiga. Making Shadow Pokemon. A bit crueler than Snagem. The organization is really big. (I never really playd the game but read a bit of the info.)
I'd have to say that its a Tie between Cipher and Team rocket.