Why is honey different colours?

Four causes, in order of importance

1. The plant. Nectar pigments, phenolics and minerals vary enormously between species, and a nectar rich in them makes a dark honey regardless of anything else.
2. Mineral content. Honeydew honeys are dark because the sugar passed through a sap-feeding insect and picked up minerals on the way. Conductivity tracks colour closely enough that regulators use it as the honeydew boundary.
3. Age. Every honey darkens slowly as sugars and amino acids react, and faster when it is warm.
4. Heat during processing. Pasteurisation and repeated warming darken honey directly and permanently, and raise HMF as they do it.

What colour predicts

Mineral content, strongly. Antioxidant content, strongly as a laboratory measurement. Flavour intensity, loosely — the rule that darker means stronger is useful and fails about one time in six, with ivy pale and bitter at one end and jarrah dark and caramel at the other. And quality, not at all, in either direction.

The most useful way to use colour is as a consistency check rather than a quality signal. Acacia is the palest honey in commerce; a golden jar labelled acacia is worth a question. Manuka is mid to dark amber; a pale one is worth a question too.