Pikmin

Pikmin are a plant-animal hybrid species and the namesake of the video game series they star in, Pikmin. These beings inhabit the planet PNF-404, and spend time buried in the ground, with their leafs sticking out. In the series, they are plucked out the ground by the player to use in battles and such. They have made crossover cameos in Mario games a few times, but their most important role was with the introduction of Captain Olimar as a playable fighter in Super Smash Bros. Brawl.

Mario Golf: Toadstool Tour
The Pikmin's first appearance in the Mario franchise was in Mario Golf: Toadstool Tour. Here, if the golf ball landed in a patch of flowers, Pikmin would pop out.

Mario & Luigi: Superstar Saga
Olimar, along with a group of Pikmin were going to appear in this game when a new type of coffee was made. He would call Mario 'Marlio', an anagram of Olimar and mistake Luigi for a dangerous beast and order his Pikmin to attack him.

Super Smash Bros. Brawl
Pikmin serve Captain Olimar in Super Smash Bros. Brawl. Although they are technically not playable, Olimar is almost completely helpless without them, for they are featured in all of Olimar's Special Moves, smash attacks, aerial attacks (except for his neutral aerial), and grabs. As such, they must be plucked from the ground. When Kirby gets Olimar's ability, he can also use Pikmin, but after plucking them, he immediately throws them.

The Subspace Emissary
A group of Pikmin start to attack a giant R.O.B. which simply rises its arms and spins around knocking them all off and kills most of them. Captain Olimar is shocked and scared, however his Red Pikmin informs him of a new visitor. The Blue Falcon speeds through the forest. Captain Falcon jumps out of the car, and Falcon Punches the robot, sending it flying away. Landing after his attack, Captain Falcon accidentally kills many of the Pikmin, but teams up with Olimar, regardless; and the pair run along some old ruins fighting the Subspace Army. They notice an Arwing attacking the ship carrying Donkey Kong: Falco Lombardi drops Diddy out of his Arwing, and with his Peanut Popguns, the monkey shoots the ship holding Donkey Kong. Captain Falcon and Captain Olimar run to assist.

Super Smash Bros. for Nintendo 3DS / Wii U
Pikmin return as Olimar's aids in Super Smash Bros. for Nintendo 3DS / Wii U. This time, Olimar appears as "Olimar & Pikmin" on the character selection screen, unlike in Brawl, where he was listed simply as "Captain Olimar".

Olimar can only have three Pikmin following him unlike the predecessor which allowed six. His up-B attacked now involves being carried by winged pikmin. The more Pikmin Olimar has following him, the slower the Winged Pikmin will fly.

WarioWare series
Pikmin later appeared in a Pikmin 2 microgame in WarioWare: Smooth Moves, which belonged to 9-Volt. Here, the player controls Empress Bulblax and must roll over all of the Pikmin to squish them before the time runs out. However, it will get harder. The Pikmin will grow larger and start jumping over the player.

In the WarioWare D.I.Y. Microgame Pikmin, the player controls Captain Olimar, who is holding a Red Pikmin in his hand. The point of the game is to throw the Pikmin onto the rock that contains nectar. If time runs out or if the Pikmin is accidentally thrown into the water, the game ends in a loss.

Luigi's Mansion
A trailer for the first Pikmin game appears in Luigi's Mansion's option screen. The trailer, predictably, includes the species of the same name.

Super Smash Bros. for Nintendo 3DS / Wii U
Blue indicates the Trophy or description is exclusive to the Wii U version.

Trivia

 * A group of Pikmin appears on a Character Card packaged with the Nintendo 3DS, one of five (which also feature Nintendo characters) used with the Augmented Reality Games software.
 * Five of the colored varieties of Pikmin each represent one of the five recognized senses; red Pikmin have noses (smell), yellow have ears (hearing), blue have mouths (taste), purple have fine hairs on their heads representing touch and white Pikmin have superior sight to the others.
 * In the Pikmin Short Movie "Occupational Hazards", a red Pikmin is seen going through a Warp Pipe while collecting some Coins, then emerging with dust forming Mario's hat and mustache on its face. Sound effects and the first seven notes of the Ground Theme from Super Mario Bros. can also be heard.