Skyward Sword
Goddess Cubes can be found throughout Hyrule in Skyward Sword but are first introduced by a Goron named Gorko. You will meet Gorko soon after landing on The Surface. He will tell you that he is intrigued by ancient artifacts such as Goddess Cubes and that he has been studying them for quite some time.
He informs Link that a "Skyward Strike" is said to activate the Cube. Upon doing this, the cube will slowly glow and then radiate a glowing light into the sky. Gorko will be amazed at what you did and demand more answers to which Link is not yet sure.
Once in the sky again, however, Fi will tell Link that it has noted areas of energy nearby. Link's map will be marked and "Goddess Chests", respective to which Cubes you have unlocked, will be able to be opened. Goddess Chests correspond to the Cubes that Link has found.