Runes are magical orbs that contain various magical spells. Some runes are common such as fire and water runes. Other runes are very rare and can only be found on one character per game such as wrath or charm. Though the exact nature of where all runes come from is never explained in the series, most runes are said to be derived from the 27 True Runes and are simply minor emanations from them. So far in the series, there are four known types of runes: True Runes, Unique Runes, Common Runes, and then a fourth class that doesn't quite fit anywhere.
True Runes are the 27 Runes that were born when Sword and Shield clashed in the creation myth. These runes are extrememly powerful and possess wills of their own. They govern the powers and emotions of the world and grant their bearers agelessness and immortaility.
See True Runes for more info.
Are one of a kind runes that are directly created from one of the 27 True Runes. These runes also seem to possess a will of their own, but this will can be subjagated if need be by a powerful runemaster like Jeane. These runes possess awesome powers of their own that rival that of the True Runes, but these runes do not give the power of agelessness like their parent runes. So far, there are only three known runes in this class.
These type of runes make up the bulk of the known runes in the series and they can be purchased in shops, scavenged from monsters, or even be the focal point based around schools of martial training or special villages. These runes do not appear to have any will of their own but their powers can only be fully realized by those who have proper affinities or training with the rune. Many of these runes are derived from the True Runes, while others appear to be man made.
There is only one set of runes that fall in this category and that is the Bright Shield Rune and the Black Sword Rune. These two runes are each one half of the True Rune the Rune of Beginning but in their seperated state they do not garner the benefits of a True Rune. Jowy states that the runes actually drain the life force of their weilder when they are used and the runes are never referred to as True Runes throughout the course of Suikoden II.
According to Suikoden V Runes are the powers of the world competing and co-exsisting of the world (such as fire and water).