Rune Shops refer to the building where runes can be bought and attached by Rune Masters. Rune shops can also have someone inside who is skilled in creating Rune Scrolls or assembling a broken rune. They are less common than Inns, but just the same are fairly common. As with inns various shops charge various prices for runes. Also Jeane is always going to be your rune shop owner once you've recruited her.