Skyward Sword’s Goddess Cubes are optional collectibles distributed throughout the Surface regions — activated by striking them with a Skyward Strike — that unlock chests floating in the Sky region, each Cube corresponding to a specific Sky chest at a specific island.
The cube-chest system is Skyward Sword’s most geographically distributed puzzle: solving a Surface cube requires remembering to search for its reward in the Sky on the next aerial segment. The game does not map which cube corresponds to which chest, requiring the player to either explore both regions systematically or accept that some rewards will remain unknown.
The reward for every Goddess Cube is a specific item: rupees, seeds, or in several cases equipment pieces and map fragments. No Goddess Cube reward is essential for completing the main quest. Several are significant upgrades that reduce the difficulty of the game’s later sections — particularly the Life Medal, which adds a heart container without any Temple completion.
Skyward Sword’s gratitude crystals — a parallel optional system where NPCs in Skyloft give crystals in exchange for resolving their problems — combine with the Goddess Cube system to fund purchases from the Moonlight Merchant. Players who engaged with both systems had access to equipment that the main game never directs them to seek. The two optional systems are designed to reward players who treat Skyloft as a community rather than a waypoint.

This is exactly why I love this game. So many layers underneath the surface if you just take the time to look.
Stumbled across this on a late-night session and couldn’t believe it. Your explanation finally made it click.