Instructions
Press the "Start" button to bring up the main in-game menu.
Highlight "Bag" on the menu and press the "A" button to get to the bag inventory screen. The bag has eight separate pockets on it and one of them is devoted entirely to Pokeballs.
Press "Left" or "Right" on the directional pad to highlight the Pokeball pocket and bring up the list of Pokeballs you are currently carrying.
Press "Up" or "Down" on the directional pad to highlight the name of the Pokeball you want to throw away.
Press the "A" button to bring up a menu that gives you the option to either "Give" or "Toss" the highlighted item. Select "Toss" to throw away the selected Pokeball. If you are carrying more than one of that specific type of ball, you are given the option to choose how many you wish to throw away.