Team Rocket just appalled me. They were dirty and greedy, but hardly high on my "evil" radar.
Team Magma/Aqua sure shocked me with how close their plans came to fruition, had Rayquaza not been there to intervene. Messing with how the earth was formed, no matter the cost, not quite too high on my "evil" radar, as they were simply misguided and a bit bizarro.
Team Galactic had me feeling terrified for weeks after stopping their plans. They're a borderline-terrorist cult. I may be just a wimp, but wow, it was quite an extreme plan.