The runes were all flat; Fire Rune of Bashing +20 str, Molten Rune of Crits +10 str & 5 crit, Blazing Rune of Toughness +20 sta & +5 int, etc, etc. The system worked out great for keeping gear at a equal level per tier. Because all attributes were potentially useful regardless of class, one could mix & match the runes which suited their need & purpose. These runes and the components to create them were scattered... everywhere; crafted, world bosses, dungeons, rare spawns, raids, token gear, mini-games, etc.
For example, I played a priestly healing class but used runes to fashion myself as a melee tank who held threat by ranged magic attacks and mitigated damage via effective health/absorbs. The very same class however could heal and provide the raid with an endless mana battery, be a short range magic nuker, fury warrior-ish or be a CC machine.
Gear modification like that where we end up with the same relative power but skewed to different ends is ideal for me. Having players search all over the world doing many different things is just icing.