The Runes are a group of items added by Quark. They can be found in dungeons and function as Enchanted Books; they can be used to give a tool or weapon an enchantment in an Anvil. The color of the Rune used changes a tool or armor piece's enchantment overlay color.
The mod Charm also adds the ability to insert Runes in End Portal Frames (like Eyes of Ender) to color-code portals. If two End Portals have the same configuration of runes they link with each other and players can teleport between them. Twelve Runes are needed to activate an End Portal; Eyes of Ender cannot be inserted.