Basically, magic runes are a way to inscribe an item so as to make it hold magical power. The exact details will be revealed in more depth later, this is just a basic run down.
Several magical societies have their own runic systems, which vary in power and use. Most notable of these are the Dwarf/Gnomes, The Drow, The Dragons, Celestials, Devils, Yuan-Ti, Giants, Aboleths and Sun Elves/Avariels.
Runes can be combined with eachother for different effects, depending on the placement of the runes and the skill of the inscriber. So a runeword could be inscribed on a weapon to make it flare with fire energy for extra damage against any drow foes it strikes, or a mistake during the inscription could result in a weapon that damages it's owner every time he hurts a drow. Runewords themselves are varied and their combinations are not always predictable.
To Craft magic runes a prospective inscriber needs the Craft Runeword feat. His skill at doing so is determined with a Runecraft skill. Runecraft gets a synergy bonus from spell-craft, and the appropriate knowledge and craft skills. So a runecrafter who wishes to put a fire effect on a weapon, would recieve synergy bonuses from Knowledge (The Planes) and Craft (Weaponsmithing).
Further details to come.