Runes are lasting enchantments placed on objects or people. Their power eventually fades over time and must be re-cast. Runes tap into magic at its source, the very power gods wield. Perhaps this is what makes rune casting so difficult. Because runes tap into this primordial power, they are less effected by other magic.
Runes take much longer to cast than other spells, measured in hours, days and even years.
Power words, on the other hand, because of their instantaneous nature, do not have the resistance to magic that runes do, but are cast almost instantly. The runecaster uses these words when he needs an immediate effect. They are so powerful, being linked to the primordial magics, that they allow no saving throw. The elves are inherently enchanted creatures, and those few who are strong enough in spirit, can utilize their inherent power, called Laereth or Glaymar to the high elves. These high magi are rare and said only to exist on Evermeet, the homeland of the elves.