From the Super Mario Wiki
In The Super Mario Bros. Super Show! episode, "Too Hot to Handle," a pineapple patch grew on Waki-Waki. Mario, Luigi, and Toad used the pineapples as projectiles against King Koopa's Shy Guys in the same manner they used vegetables in Super Mario Bros. 2.
Donkey Kong uses smaller Pineapples when fighting the Tusk bosses. He must pick up a Pineapple, which is done by clapping when near one, and throw it at the Tusks. Sometimes, they will hit the Tusk's body and explode, other times, the Tusk will accidentally suck up the Pineapple, in which case it will explode inside of it, revealing it's heart. Later on, Pineapples appear in Iguanagon's Realm, where they are used as weapons against Iguanagon; they also appear under the same circumstances in the Star Fruit Kingdom's level Asteroid Belt. Evil birds throughout Donkey Kong Jungle Beat also use Pineapples as weapons. Like in Donkey Kong 64, these pineapples explode on contact, but also automatically detonate after a few seconds.
Pineapples appear as a fruit for Yoshis in Super Mario Sunshine. When a Yoshi eats one, it will become Orange and his juice meter will be filled. An abnormally large pineapple also appears on a local rooftop, blocking the red Warp Pipe leading to Sirena Beach. The player must use a Yoshi to eat the large pineapple and unblock the Warp Pipe before they can progress.