Pikmin

Pikmin are a plant-animal hybrid species and the namesake Pikmin series. These beings inhabit the planet PNF-404, and spend time buried in the ground, with their leaves 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 Super Mario games a few times, but most notably appeared in Super Smash Bros. series aiding Captain Olimar since Super Smash Bros. Brawl.

Mario Golf: Toadstool Tour
Pikmins' first Super Mario-related appearance was in Mario Golf: Toadstool Tour. Here, if the golf ball landed in a patch of flowers, Pikmin would pop out. In this game, they come in red, yellow, and blue, which were the only Pikmin colors at the time as Pikmin 2 had not yet been released.

WarioWare series
Pikmin appear in the microgame Pikmin 2 in WarioWare: Smooth Moves, which belongs 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, as the difficulty increases, the Pikmin grow larger and start jumping over the player. The microgame reappears in WarioWare Gold.

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.

Pikmin appear in the Pikmin 2 microgame in WarioWare: Get It Together!, though they do not have any effect on gameplay.

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 gains 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 "Pikmin & Olimar" on the Japanese character selection screen, unlike in Brawl, where he was listed simply as "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 fly.

Super Smash Bros. Ultimate
The same Pikmin from the previous installment return alongside Olimar in Super Smash Bros. Ultimate.

Super Mario Maker
Pikmin, alongside the majority of the Super Smash Bros. for 3DS / Wii U cast, cameos as one of the costumes Mario can obtain in Super Mario Maker via the Costume Mario power-up. Pikmin sound effects can be heard, the "lose a life" tune is replaced by the Pikmin's own death cries, and the "Course Clear" fanfare is replaced by the tune that plays after obtaining an important item in Pikmin 3. Pressing causes the red and blue Pikmin to mature into flowers. When underwater, all three of them are encased in a bubble.

Super Nintendo World
Several Pikmin appear on the artwork used for the bags in the Super Nintendo World theme park land and can be found hidden on ledges throughout and as an hidden animation viewed through the augmented reality Binoculars. Some of these hidden Pikmin are seen working together carrying items such as a Coin and a fruit.

The Super Mario Bros. Movie
In The Super Mario Bros. Movie, a statue of a Pikmin appears in the Brooklyn Couple's residence.

Other appearances
A trailer for the first Pikmin game featuring the eponymous species appears in Luigi's Mansion's option screen.

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

In the Wii to Wii U system transfer application, Pikmin appear to carry the user's data.

Super Smash Bros. for Nintendo 3DS / Wii U trophies
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.