Example Panels style plugin with substyles. You add this to your module or theme in the normal way for ctools / panels plugins. FIlename should end in .inc.

example_style.inc.php

<?php

/**
 * @file
 * Definition of the 'bootstrap_style' panels style plugin.
 */

$plugin = array(
  'title' => t('Example Parent Style'),
  'description' => t('Example style providing substyles'),
  // We offer substyles so provide callbacks to do so.
  'get child' => 'example_style_get_substyle',
  'get children' => 'example_style_get_substyles',
  'settings form' => 'example_style_settings_form',
  'pane settings form' => 'example_style_settings_form',
  'defaults' => array(
    'first_option' => '',
    'second_option' => '',
  ),
);

/**
 * Provides List of substyles.
 */
function example_style_load_substyles($substyle_name = NULL) {
  $substyles = array(
    'first' => array(
      'name' => 'first',
      'title' => 'First Substyle',
      'panes' => TRUE,
      'regions' => TRUE,
    ),
    'second' => array(
      'name' => 'second',
      'title' => 'Second Substyle',
      'panes' => TRUE,
      'regions' => FALSE,
    ),
  );
  if ($substyle_name) {
    return $substyles[$substyle_name];
  }
  return $substyles;
}

/**
 * Merge the main style plugin with a substyle to create a sub plugin.
 */
function example_style_merge_plugin($plugin, $style_name, $substyle) {
  $plugin['name'] = $style_name . ':' . $substyle['name'];
  $plugin['title'] = 'Example: ' . check_plain($substyle['title']);
  $plugin['substyle'] = $substyle;
  if (!empty($substyle['panes'])) {
    // Make this substyle show up as a pane style.
    $plugin['render pane'] = 'example_style_render_pane';
  }
  if (!empty($substyle['regions'])) {
    // Make this substyle show up as a region style.
    $plugin['render region'] = 'example_style_render_region';
  }
  $plugin['weight'] = 0;
  return $plugin;
}

/**
 * Callback to provide a single substyle.
 */
function example_style_get_substyle($plugin, $style_name, $substyle_name) {
  $substyle = example_style_load_substyles($substyle_name);
  return example_style_merge_plugin($plugin, $style_name, $substyle);
}

/**
 * Callback to provide all substyles.
 */
function example_style_get_substyles($plugin, $style_name) {
  $data = example_style_load_substyles();
  foreach ($data as $id => $substyle) {
    $substyles[$style_name . ':' . $id] = example_style_merge_plugin($plugin, $style_name, $substyle);
  }
  return $substyles;
}


/**
 * Theme fuction for the region styles.
 */
function theme_example_style_render_region(&$variables) {
  $output = '';
  $settings = $variables['settings'];
  $panes = $variables['panes'];
  $style = $variables['style'];
  $substyle = $style['substyle'];

  switch ($substyle['name']) {
    case 'first':
      // Here you could call your own theme function.
      $output .= '<div style="border: 2px dotted #aaa; padding: 20px; margin: 20px">';
      $output .= '<h4>Region: First Style</h4>';
      $output .= '<div>First Option: ' . $settings['first_option'] .  '</div>';
      $output .= implode(PHP_EOL, $panes);
      $output .= '</div>';
      break;
  }

  return $output;
}

/**
 * Theme function for the pane style.
 */
function theme_example_style_render_pane(&$variables) {
  $output = '';
  $settings = $variables['settings'];
  $content = $variables['content'];
  $style = $variables['style'];
  $substyle = $style['substyle'];

  switch ($substyle['name']) {
    case 'first':
      // Here you could call your own theme function or just send in some
      // style settings to the default panels pane.
      $output .= '<div style="border: 1px solid #aaa; padding: 20px; margin: 20px">';
      $output .= '<h4>First Style</h4>';
      $output .= '<div>First Option: ' . $settings['first_option'] .  '</div>';
      $output .= theme('panels_pane', $variables);
      $output .= '</div>';
      break;

    case 'second':
      // Here you could call any theme function or just send in some
      // style settings to the default panels pane.
      $output .= '<div style="border: 1px solid #ccc; padding: 20px; margin: 20px">';
      $output .= '<h4>Second Style</h4>';
      $output .= '<div>Second Option: ' . $settings['second_option'] .  '</div>';
      $output .= theme('panels_pane', $variables);
      $output .= '</div>';
      break;
  }

  return $output;
}

/**
 * Options for the Panels style plugin to help style panes.
 */
function example_style_settings_form($settings, $display, $pid, $type, $form_state) {
  $style = $form_state['style'];
  $substyle = $style['substyle'];
  $form = array();

  if ($substyle['name'] == 'first') {
    $form['first_option'] = array(
      '#title' => t('Options for First Substyle'),
      '#type' => 'select',
      '#options' => array(
        'style1' => 'Style 1',
        'style2' => 'Style 2',
      ),
      '#default_value' => $settings['first_option'],
      '#empty_option' => t('Default'),
      '#empty_value' => NULL,
    );
  }
  elseif ($substyle['name'] == 'second') {
    $form['second_option'] = array(
      '#title' => t('Options for Second Substyle'),
      '#type' => 'select',
      '#options' => array(
        'style1' => 'Style 1',
        'style2' => 'Style 2',
      ),
      '#default_value' => $settings['second_option'],
      '#empty_option' => t('Default'),
      '#empty_value' => NULL,
    );
  }
  return $form;
}