Metal Cubes are special items primarily used to increase the time that the explorer can be in another world through a portal. Three metal cubes allow an expedition to spend 100+ days in the Portal World and attain the "Beyond the gate" achievement (spending 100 days in a portal world).
A metal cube can also be used to disable shrine curses by placing it on the altar when looting. Be careful not to use the "Take All" option, as this will take you out of of the loot window without giving you a chance to place the cube. Using a cube does not prevent you from losing standing with the natives.
There is also a rare insanity event that can occur in which a companion disappears and is replaced by a metal cube.