Wooden Box

A crate is a smaller, unpushable wooden box. There are two types. One is the bigger crate, which Link has to roll into to break. The other is a smaller, lightweight crate that Link must carry and throw it or slash his sword at it to reveal its hidden contents. If anything; single recovery hearts or nominal rupees can be found inside these small boxes. Crates can be found inside of Jabu-Jabu's Belly and other various places in Ocarina of Time. There are many crates in Kakariko Village in Ocarina of Time. While looking for one of the lost Cuccos, one can be found hiding in a crate in the center of town. They are also found in various locations in Majora's Mask. In Wind Waker, they floated and because of that were used in several places to

Ocarina of Time/Majora's Mask
Smaller crates are found in different locations throught Hyrule and Termina. While they usually contain some small, useful item, their most common use is in holding down light switches (like in Jabu-Jabu's belly). They were far more frequent as item storage in Majora's Mask, being found in more numerous locations.

The Wind Waker
In The Wind Waker, crates played a more prominent role because they would float. This factor was utilized in the Tower of the Gods, when Link would get from place to place using said blocks when the water had risen. Link could move the lighter crates by picking them up on dry land, but could only stand on them when he jumped on them. When he would try and climb on while swimming, he would only push the crate.

Ocarina of Time/Majora's Mask
Bigger crates in the Ocarina of Time where found nearly everywhere, but couldn't be moved. The only thing Link could do to these very firm boxes was roll into them to break them open. These boxes almost always had money in the House of Pots, and they were a hiding place for Gold Skulltulas. These boxes were very common in the land of Hyrule. In Majora's Mask, these boxes were less common, but were found throughout the Spider Houses of Termina. They commonly held skulltulas or hid useful passages.

The Wind Waker
In the Wind Waker, the bigger crates served the same purpose as the smaller crates. They would float and holster objects. These boxes could be broken open by bombs. Link could climb onto them by pushing against them while swimming. Link couldn't lift these, so instead he would push them around.