Instructions
Remove the GameCube controller from the system. Blow into the connection port to remove any accumulated dust and debris. This could be the cause of the problem as dust or any other debris in the port will prevent the controller from making a connection to the system, thus the GameCube will not recognize the controller.
Connect the controller into a different port on the GameCube system. If the controller is still unresponsive, the problem may lie with the controller and not with the controller ports. If this is the case, you may have to replace the GameCube controller.
Inspect the end of the GameCube controller plug. Blow on the controller's connectors to remove any dust or debris. As in Step 1, if the controller's connectors have dust or grime on them, it can cause a disruption in the connection between controller and system.
Search for a professional to repair the GameCube controller ports, if after undergoing the troubleshooting process, you determine that they are indeed damaged. A professional repair person can fix this problem for you.