In the original film the idea was going to be, yellow = good and blue = bad. This got changed to blue = good and red = bad. However in tank programs, the original coloring remains. So Clu 1.0, who is a good guy, is yellow, and all of Sark's tank commanders are blue.
The coloring in the second film is different. Light blue/white - good. Orange - bad. Yellow - Clu 2.0 (very bad).