So fiction it is.
It's fashionable today to say Hydra, but that's a fad. COBRA is the better choice, if also a rather obvious one. But look, what are my criteria here? Well...
1. Doing evil for evil's sake
2. Iconic uniforms and cool named characters
3. Mind-blowingly, stupidly, epic plots against the world
4. Potential for comedy
COBRA could hit the first three easily (while another front-runner, Wolfram & Hart from Angel, would do #1 better, but fail at #2 and the COBRA acronym does stand for Criminal Organization of Bloodiness, Revenge, and Assassination, which might be enough to clinch #4. However, there's one criminal organization that's really good at #4 without compromising criteria 1 through 3. Ladies and gentlemen, I present my very favorite evil org: AIM (Advanced Idea Mechanics)!
Images from Marvel Smart Ass' A.I.M. High series.