What does the color of an egg yolk mean?

A pale yellow yolk and a deep orange one differ because of what the hen ate, specifically the pigments called xanthophylls found in things like marigold petals, corn, alfalfa, and green plants. Hens on pasture or feed rich in those pigments lay darker, oranger yolks; hens on a wheat or barley diet lay paler ones. It is a diet marker, plain and simple, and producers can even tune yolk color by adjusting feed, so a vivid yolk is not automatically a sign of a happier hen or a more nutritious egg, though pastured eggs do tend to have modestly more of certain nutrients for separate reasons.

The nutritional difference between a pale and a deep yolk is minor, and yolk color tells you nothing about freshness or safety. The related myth worth clearing up is shell color: brown eggs are not healthier or more natural than white ones. Shell color is purely a function of the hen's breed, and brown eggs often cost more simply because the breeds that lay them tend to be larger birds that eat more feed. Inside, a brown egg and a white egg from similarly fed hens are essentially identical.