Every mob has 2% chance to drop a blank rune, and some mobs can drop with effects

there's three blue slots in your inventory, the runes will only work if you place them in these blue slots.

Eternal Craft inventory

EternalCraft inventory

To add effects to a empty rune you need to add the rune to a special item look at the example:
Filling a rune

Filling a Rune

There are 18 Runes with effects, and there are 6 colors without the empty.

Runes colors

The runes are these:

Rune of the Colossus: Right click empower the ancient stone. (Yellow)

Rune of the Silence: Reduce speed loss by 50% and you will be invisible from monsters while sneaking. (Purple)

Rune of Swiftness: Increase movement speed. (Blue)

Rune of the Titan: You no longer recieve knockback. (Yellow)

Rune of the Life drain: 33% chance to restore 1 HP when attacking. (Purple)

Rune of the Unbreakable: The rune generate a shield that absorbs 9 damage. The shield is regenerated if the wearer don't take damage for 7 seconds. (Yellow)

Eternium Rune: 5% of your damage are converted into a shield that absorbs incoming damage. The shield's max health is 9 and slowly decay. (Blue)

Rune of Power: SpiritDiamond Sword's active now grants 5 bonus damage isntead of 2 when used.

Rune of the Rentless Force: Knockbacks ennemies at the activation of the Claymore of the Rentless Force and increase the duration of the active.

Seismic Rune: Increase the range and the knockback of the Bone Crusher's active. (Green)

Rune of Regeneration: Slowly regenerates the wearer's HP. (Green)

Rune of Colossal power: Increase your attack damage by 12,5% of  your maximum health. (Orange)

Rune of Growing power: Increase your attack damage by your level / 5. (Red)

Rune of Thunder: Increase the power of Eternium sword's lightning bolt. (Red)

Rune of Stamina: Increase your maximum health by 3. (Orange)

Rune of Softt Fall: You no longer take fall damage. (Blue)

Living Rune: Increases your regeneration when under 25% health. (Green)

Rune of Frenzy: While striking an ennemy you gain 1 attack damage for a short time, the bonus can stack up to 9 times. (Red)