Generally color swatches are paired to give a suggestion for a complementary or accent color that is determined according to prevailing color theory. Sometimes you'll see the primary color with 2 to 4 other swatches, depending on the color relation used (tertiary, complementary, etc).
I use compass-colors to apply this concept to my stylesheets.
The Flat UI's Color Swatches look delicious and I'd like to learn to use them.