Using hook_theme

/**
 * Implementation of hook_theme().
 */
function example_theme() {
  return array(
    'example_taxonomy' => array(
      'template' => 'example-taxonomy',
      'arguments' => array('node' => NULL, 'options' => NULL),
    ),
    'example_taxonomy_terms' => array(
      'arguments' => array('voc' => NULL, 'node' => NULL, 'options' => NULL),
    ),
    'example_front_page' => array(
      'template' => 'example-front-page',
      'arguments' => array(),
    ),
  );
}