ben_danger: The method I used for the clip shown was to go in frame by frame and paint the lightsaber a different tint by hand. The program I used was Bauhaus Mirage (the predecessor to TVPaint), which is kinda like a mix between Photoshop and After Effects. Granted, it's not the fastest method, but it gives me the best and most accurate results (using vector masks in Vegas was a lot quicker, but the final image isn't as good-looking in my opinion).
Octorox: I thought about making it green, but for the Twilight of the Republic (AofC) edit, I kinda wanted Dooku's lightsaber to be a different color than either Anakin's or Obi-wan's. Because of that, I carried over the same purple lightsaber over to the The Black Knight Rises (RotS) edit to maintain series continuity.