Mario rides this airplane only in World 4-3 of Super Mario Land, where the level autoscrolls and you can fly in any direction and shoot unlimited amounts of ammunition.
In Yoshi's Woolly World, one of Yoshi's transformations is Sky Pop Yoshi, and essentially has the same gameplay as the original Sky Pop.
In Mario & Wario, the cutscene after Level 10 shows Yoshi flying the Sky Pop.
In Super Mario Maker, an event course was made which contained an event costume of the Sky Pop. The level was made for Southwest Air, an air travel company. The costume retains all of the sprites and sounds from the original Super Mario Land.