From the Super Mario Wiki
They appeared again in Super Mario World 2: Yoshi's Island and its remake Yoshi's Island: Super Mario Advance 3. This time, can be broken by Ground Pound to open them and release either Stars or a Key. Balloons hold crates in the air, and they can be shot down by a Yoshi Egg.
The Crate later appears in Super Mario 64. They are items that can be picked up and thrown at an enemy, usually containing Coins. A different, specific crate appears in Jolly Roger Bay on the bridge of the sunken ship. This specific crate is larger and has a darker shade of color. It slides on the bridge of the sunken ship. Being hit by such crate causes a lose of life.
Crates also are in the Donkey Kong series with the notable Animal Crate where an Animal Buddy can be obtained. In Donkey Kong Country 2: Diddy's Kong Quest, they are thrown like Barrels, but break on contact, much like the Vine Barrel from Donkey Kong Country.
A Crate is also an item container featured in the Super Smash Bros. series. Like all other containers, the Crate must be broken before the items inside can be used in battle. To break the carrier, the wooden Crate can either be picked up and tossed in the air, or be attacked repeatedly on the ground. Crates can also be thrown at opponents, although it is difficult to hit other fighters, as throwing the cumbersome container took a long amount of time. Sometimes, Crates explode under enough stress, damaging all nearby fighters. In the original Super Smash Bros., the Crate holds one to three items, and is also extremely heavy. In fact, only Donkey Kong can lift up the Crate and walk around with it; all the other fighters can only pick up the container and toss it while they stay still.
In Super Smash Bros. Melee, the Crate's carrying capacity is increased, revealing anywhere from three to five items when broken. The Crate is still very heavy, although all fighters can pick up the container and walk with it (albeit most can only walk very slowly because of the container's weight). Again, only Donkey Kong can walk at a relatively normal speed with a Crate in hand.
Crates also appear on Isle Delfino in Super Mario Sunshine. They can only be destroyed by ground pounding them, which typically reveals a coin. In addition, there is a man in Delfino Plaza named the Crate Guy, who has crates stacked in various patterns. If Mario walks into his building, the player can talk to him and is given the option to play a minigame, which involves destroying all the crates in the room in thirty seconds. Doing so successfully reveals to the player a Shine Sprite.
The Crate, along with the Barrel, returns in Super Smash Bros. Brawl. However, this time it changes its appearance depending on the environment. For example, if it is in a Star Fox stage, it turns into a chrome Crate. This does not change its effect, however. The game also introduces the Rolling Crate, a Crate that slides across the floor, and the Blast Box, a dangerous item that can explode if it is thrown.
The crates from the first game also appear in Super Mario Galaxy 2 and shares the same function as the first game. They appear in secret missions for the Rightside Down Galaxy and the Upside Dizzy Galaxy. During these missions, Mario, as Fire Mario, must destroy all the crates on the platform within twenty seconds in order to get a Power Star in the Crate Burning minigame. There are also metal-edged variants of crates, which are a little different to the normal ones. These ones are a bit stronger - once a fireball (from Fire Mario or Fire Luigi) destroys one, the fireball disappears instead of burning through it and destroying other crates in the way like the normal ones.
Crates, having the same design as the ones from the Super Mario Galaxy games, reappear in Super Mario 3D Land. Mario can break them by rolling into them, or throwing them with fireballs or boomerangs. They may also be destroyed by running through them while invincible.
 Super Smash Bros. Melee Trophy
 Super Smash Bros. Brawl Trophies