This page lists all the known Secret Worlds in Metroid Prime 2: Echoes. Secret worlds that require Floaty Jump are included in this list, as the only known way of activating this glitch is inbounds before the Chykka fight.
Temple Grounds (Sky Temple Grounds)
Great Temple (Sky Temple)
Agon Wastes (Dark Agon Wastes)
Torvus Bog (Dark Torvus Bog)
Sanctuary Fortress (Ing Hive)
Rooms in this list either require being Out of Bounds first, thus not a "true" Secret World," or are in Multiplayer only.