Throw an apple right between two Magmar, and they will fight over it, knocking each other out with fire breath.
The River stage is a cornucopia of comedy. We have Bulbasaur's "Bul-ba!" when it gets hit with a Pester Ball, the Slowpoke, and the funniest part of the stage is Psyduck. If you hit the yellow ducky with an apple or a Pester Ball, it sinks into the water, but it'll continuously pop out of the water and quack.
The Cave stage has the Ditto posing as Bulbasaur, as well as Pikachu being kidnapped by a Zubat. If you rescue Pikachu by pelting Pester Balls at Zubat, it'll fly down on balloons.
Jigglypuff getting upset at players who interrupt her singing by either throwing an apple or playing the Poke Flute.
The Mankey in the Valley stage.
Upon entering the Valley, three Squirtle swim in front of the vehicle. They show up again later to knock a Mankey off a cliff, as if he were a bowling pin.
The sound Pikachu makes after he eats Pokémon food. CHAAAAAAAAAAAAAAAAAAAAAAAAAAAA!