CSI LV: I'm going with Natalie Davis: criminally insane and yet very sympathetic and awesome. And Hannah West: completely sociopathic -- and awesome, and more than half the age of the criminalists she kept foiling. Forget the show, they're pretty much my favourite villains in the franchise. I was glad when they were taken down (or in Hannah's case, got some serious comeuppance), but I loved watching them in action.
CSI Miami: Clavo Cruz. He wasn't even that diabolical (comparatively) until his final episode, but the best and most frustrating thing about him was how he kept slipping out of trouble. He was so good at it. You could just see how he got under Horatio's skin like no one else because of it, and I have to admit it was fun seeing Horatio that irritated by something he couldn't instantly fix. Wish they hadn't killed him off, there isn't even a runner up as far as favourite Miami villains go.
CSI NY: Has a huge pick of good villains, so I'm choosing two and a half. Shane Casey and Suspect X. The half is Henry Darius, because I only saw his one episode in New York (where he was compelling and damn scary), but I know he started off in Miami.