When you export your application as a Runnable JAR use the + Library handling: Copy required libraries into a sub-folder next to the generated JAR or + Library handling: Package required libraries into generated JAR
More information is available in the jogamp jogl wiki: http://jogamp.org/wiki/index.php/Setting_up_a_JogAmp_project_in_your_favorite_IDE http://jogamp.org/wiki/index.php/JogAmp_JAR_File_Handling
Also you will need to use the java -jar yourapp.jar command line option to run your application.