Check out the official runestones page on the D3 website.

There are five runestone types: Crimson, Indigo, Obsidian, Golden, and Alabaster. Each runestone affects skills differently. For example, adding a Crimson Runestone to a skill may enhance its damage, while adding an Alabaster Runestone might add a stun effect.

In addition to their color, runestones also come in different ranks of power; the higher a runestone’s rank, the more dramatic its effect on the skill. Experiment, and discover which skill and runestone combination best suits your personal playstyle.
I'm not sure what each rune is intended to enhance other than Crimson=damage but augmenting active skills 5 different ways seems like a great way to add depth to what can be considered a straightforward game (point, click, kill, repeat).

I'm excited

Diablo III - Runestones