Red, of course, is the color of a Sith's lightsaber; it also suggests that you should have a bad feeling about this. When the Clone Wars cartoon began with a red logo, it signified that Darth Maul was about to show up. Two other Star Wars movies had red logos -- and they happened to be the movies that wiped out the Sith and the Jedi, respectively.

The earlier movie used a yellow logo to represent the light. This time, red denoted the dark side. The color change of the logos works well in tune with the films while effectively communicating the themes and modulation of each one.