We all know about Team Rocket, Team Magma and Team Aqua. Here you can come up with your own evil organization, have fun with it.

For Example:

The Foot Clan:

The Foot is an ancient organization of pokemon hunters, their goal is to rid the world of all pokemon. They have found ways to render their powers useless and found ways to capture them. They are ruthless, evil and mercless, in addition to eliminating pokemon, they also plan to conquer the world. Although they hunt pokemon, there are some pokemon who serve the Foot to save themselves. The Foot are led by a man named Oroku Saki aka The Shredder.

Note: Yes, I borrowed this from TMNT, but i liked it.

P.S. For a brief time, Ash was one of them, but decide he had enough and just left.