How does one flush rules on theme activation or deactivation only?

While the solutions provided here do still work, WordPress has evolved since and does now (since 3.3, I believe) provide direct hooks for theme activation.

after_switch_theme will fire on theme activation and switch_theme before deactivating an old theme.

Hence the up-to-date answer is:

function reflush_rules() {
    global $wp_rewrite;
    $wp_rewrite->flush_rules();
}
add_action( 'after_switch_theme', 'reflush_rules' );