You can de-register and de-queue WordPress loaded javascripts and CSS styles by passing them into the wp_print_scripts function. This can help with fewer server requests if the scripts are no longer required or if a conflict is occurring.

So for example if I wanted to remove the WordPress Twenty Twelve default mobile menu javascript you would use:

//Remove 2012 Mobile Javascript
function de_script() {
    wp_dequeue_script( 'twentytwelve-navigation' );
    wp_deregister_script( 'twentytwelve-navigation' );
}

add_action( 'wp_print_scripts', 'de_script', 100 );

You just need to know what name was used to register and enqueue it.