There really isn't any. You can revisit every dungeon after completing it, and all items stay right where they are if you don't get them. Except for ONE exception. In the West Shrine. You can use turtle snacks for a certain section for an armor and more turtle snacks. But if you use all your snacks before then it can be missed. The armor is purchasable in Mirage Village however, so it's not a big deal. "What is a man? A miserable little pile of secrets."
Though I like the game, it's frustrating that items can be anywhere: in walls, on the floor, in puddles, virtually anywhere. A FAQ is probably the only way to get everything without walking up to each surface pressing C.
Chao, Chao Owner 3: Enjoying the time we've been given here on Earth is the most important thing of all.