Wooden Box

A crate is like a box except it is smaller and cannot be pushed. Instead, Link must carry it and throw it or slash his sword at it to reveal its hidden treasures. Mainly low priced rupees or a heart. You can find them inside of Jabu Jabu's Belly in Ocarina of Time

=Majora's Mask= In Majora's Mask, one of the Bombers hide in one of the crates to Eastern Clock Town to get away from Link. Link can also hide in these crates, but he was to be crouched down so you can't see his head/hat.