Runes are a sort of pass that allow you to gain entry into one of the 8 shrines.  If you don't have the rune, you can't enter.  Fortunately, most of the runes are located within their corresponding town.
Where Location Visual Description
Moonglow Go to the NW part of town (where Mariah is waiting) and search 3 spaces South of the brick square.
BritainGo into the inn and search at the foot of the stairs (one square to the right).
JhelomRequires 'Key'.  Go into the inn, and head west until you reach a door and go through it.  In the next room, search the west wall for a fake wall and go through it.  Head down and go down the stairs.  Immediately go up and search the north wall for another fake wall and walk through it.  Head through the corridor and up to the other side until you're in a room with a ghost.  Talk to him and tell him 'Yes' and he will tell you to search for the Rune in the corner of this room.  Search the bottom-left corner (on the damage floor).

Note~You technically don't have to talk to the Ghost in order to pick up the Rune of Valor.
YewRequires 'Key'.  Go across town and go up into the court house (last building going up).  Head west into the next room and go up the stairs.  Go up, and use Key to open up the jail cell with someone in it.  Search the bottom-right corner of the cell.
MinocHead to the other side of town and go down into the Weapon Shop.  Head east into the next room of Zircon the Smith.  Walk into the damage floor area and search in the top-right corner.
TrinsicWalk to the other side of town to where the equipment shop is and go south.  Head into the fenced in area where a man is standing.  Search the crop field (from standing in front of the old man, 2 spaces right, 1 space down).
Castle BritanniaWalk into the castle and head up.  At the junction head left.  At the next junction head up.  Walk up a little ways, and walk into the small room on the right side.  Search the right side of the room for a fake wall and go through it.  Search the empty area between the 3 treasure chests.
PawsRequires 'Key'.  Walk to the other side of town and enter the bottom most building (Stables).  Use the key to open the door and go through to the other side.  Head across the fence and head down into the small area at the bottom (2x2 area).  Search the bottom-right square.
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