Mostly, I think, ruins are utilized to give a sort of mystery and enigma to a setting, usually to imply that there was once something great before people marched on, or some terrible catastrophe happened. It can be used to hint at power that is now unknown, such as the magic doors of Zeal in the future, the many sealed boxes, and the Forest Ruins on Medina. To support the more tragic end of things, you have no further to look than either the Giant's Claw being formed of the Tyrano Lair, or in Chrono Cross, the Dead Sea, the latter being so earth-shakingly disastrous that time itself ceased to exist there anymore, for the most part.
