From the Super Mario Wiki
Super Mario World 2: Yoshi's Island / Yoshi's Island: Super Mario Advance 3
Goonies made their debut appearance in Super Mario World 2: Yoshi's Island. They appear in most mountain levels and are always found in groups. There are many different varieties of Goonies. There are Flightless Goonies which, as the name implies, are Goonies that cannot fly and run on the ground. There is a Dry Bones-like variety of Goonie, known as the Skeleton Goonie, which usually carries bombs. Bowling Goonies are fat Goonies that roll along the ground. Very Goonies are the flying versions of Bowling Goonies, and if Yoshi swallowed one of these and spat it out, it would turn into their flightless counterparts. Additionally, Goonies can be seen flying in the background in some levels (as seen in the image on the right).
Yoshi Touch & Go
In Yoshi Touch & Go, Goonies are occasionally seen flying in the sky in some parts during the ground part of the Marathon mode. Yoshi can hit them with eggs to earn points. Skeleton Goonies also appear.
Yoshi's Island DS
Goonies also appeared in Yoshi's Island DS, along with their flightless and skeletal counterparts. This game has two levels named after Goonies: Goonie Heights and The Goonie Coast Isn't Clear! A Very Goonie boss named Moltz the Very Goonie also appears as the fort boss of World 5.
Game & Watch Gallery 3
In Paper Mario, during the cutscene where Mario rides the Whale to Lavalava Island, a Goonie can be seen flying over the ocean. Unlike most characters in Paper Mario (one of the few other exceptions being the Whale himself), this Goonie was three-dimensional.
Mario Kart: Super Circuit
Goonies made a cameo appearance in Cheep-Cheep Island in Mario Kart: Super Circuit. They don't serve as obstacles to slow down the racers - they simply fly away temporarily if the player drives into one.
Goonies appear in Super Smash Bros. Melee and Super Smash Bros. Brawl in the background of two Yoshi stages: Yoshi's Story from Super Smash Bros. Melee and Yoshi's Island from Super Smash Bros. Brawl. Goonies also appear as a Sticker in Super Smash Bros. Brawl.
Mario & Luigi: Bowser's Inside Story
Goonies have a very minor appearance in Mario & Luigi: Bowser's Inside Story during the Bowser's Castle fight. When Bowser attacks, Goonies occasionally fly out from under the castle.
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