The colors of the various files found by System Cleaner indicate at what group of junk files the individual file found belongs. You can change or see which ones correspond to each color on the Temporary Files options.

Click on "Options" (left program menu), Select Temporary Files - Type of Files.

NOTE: As of version 4.8 we disabled the color coding option. We were not happy with the performance so we decided to remove it until we optimize it in order to keep everything running at full speed, as our customers have grown used to.