Ctools Content Type for Panels (pane). Adding stylesheets and scripts in pane. Variables can be set in pane, and extended to scripts. Markup is stored in a standard template file, with parsed variables.

markup.tpl.php

<?php
/**
 * @file
 * Markup template.
 * This is placed in: my_module/plugins/panes/resources/
 */
?>

<div>
    <div class="my_output"></div>
</div>

my-script.jquery.min.js

/**
 * @file
 * Custom jQuery script
 * This is placed in: my_module/plugins/panes/resources/js/
 */
 
(function($, settings){
  
  console.log(settings);
  $('.my_output').append('<p>Resource base: ' + settings.my_pane.resource_base + '</p>');
  $('.my_output').append('<p>Module path: ' + settings.my_pane.module_path + '</p>');

})(jQuery, Drupal.settings);

my_module.info

name = My Module
description = Ctools Content Type Example
core = 7.x
package = Panes

dependencies[] = ctools

my_module.module

<?php
/**
 * @file
 * Custom module to create custom Panel panes.
 */

/**
 * Implements hook_ctools_plugin_directory().
 * Looks for ctools content type (pane).
 */
function t2_juleaktivitet_ctools_plugin_directory($owner, $plugin_type) {
  if ($owner == 'ctools' && $plugin_type == 'content_types') {
    return 'plugins/panes';
  }
}

my_pane.inc

<?php
/**
 * @file
 * Panels pane.
 * This is placed in: my_module/plugins/panes/
 */

/**
 * Pane settings.
 */
$plugin = array(
  'single' => TRUE,
  'title' => t('My Pane'),
  'description' => t('This is my pane.'),
  'category' => t('Custom panes'),
  'admin info' => 'my_pane_admin_info',
  'edit form' => 'my_pane_edit_form',
  'render callback' => 'my_pane_render_pane',
  'no title override' => TRUE,
  'defaults' => array(
    'my_variable_1' => NULL,
    'my_variable_2' => NULL,
  ),
);

/**
 * Callback: Pane info.
 */
function my_pane_admin_info($subtype, $conf, $contexts) {
  if (!empty($conf)) {
    $block = new stdClass;
    $block->title = 'My pane.';
    $block->content = t('<p>This is some info on the pane.</p>
      <ul>
      <li><u>My variable 1:</u> <em>@my_variable_1</em></li>
      <li><u>My variable 2:</u> <em>@my_variable_2</em></li>
      </ul>', array(
      '@my_variable_1' => $conf['my_variable_1'] ? $conf['my_variable_1'] : 'Variable 1 is not defined.',
      '@my_variable_2' => $conf['my_variable_2'] ? $conf['my_variable_2'] : 'Variable 2 is not defined.',
    ));
    return $block;
  }
}

/**
 * Callback: Render pane.
 */
function my_pane_render_pane($subtype, $conf, $args, $context){
  $resource_url = str_replace(DRUPAL_ROOT . DIRECTORY_SEPARATOR, '', dirname(__FILE__)) . '/resources';

  _my_pane_include_style($resource_url);
  _my_pane_include_javascript($resource_url, $conf);

  $markup = file_get_contents(DRUPAL_ROOT . DIRECTORY_SEPARATOR . $resource_url . DIRECTORY_SEPARATOR . 'markup.tpl.php');
  
  $content = ctools_context_keyword_substitute($markup, array('%resource_base' => $resource_url), $context);

  $block = new stdClass();
  $block->content = $markup;

  return $block;
}

/**
 * Callback: Edit form.
 */
function my_pane_edit_form($form, &$form_state) {
  $conf = $form_state['conf'];

  $form['my_variable_1'] = array(
    '#title' => t('Variable 1'),
    '#description' => t('Here you can define variable 1.'),
    '#type' => 'textfield',
    '#default_value' => $conf['my_variable_1'],
  );

  $form['my_variable_2'] = array(
    '#title' => t('Variable 2'),
    '#description' => t('And here you can define variable 2.'),
    '#type' => 'password',
    '#default_value' => $conf['my_variable_2'],
  );

  return $form;
}

/**
 * Callback: Submit form.
 * Stores data in conf.
 */
function my_pane_edit_form_submit($form, &$form_state) {
  foreach (array_keys($form_state['plugin']['defaults']) as $key) {
    if (isset($form_state['values'][$key])) {
      $form_state['conf'][$key] = $form_state['values'][$key];
    }
  }
}

/**
 * Include stylesheets.
 */
function _my_pane_include_style($resource_url) {
  drupal_add_css($resource_url . '/css/main.style.css', array(
    'group' => CSS_DEFAULT,
  ));
  drupal_add_css($resource_url . '/css/ie.style.css', array(
    'group' => CSS_DEFAULT,
    'preprocess' => FALSE,
    'browsers' => array('IE' => 'lte IE 8', '!IE' => FALSE),
  ));
}

/**
 * Includes Javascript / jQuery.
 */
function _my_pane_include_javascript($resource_url, $conf){
  drupal_add_js(array(
    'my_pane' => array(
      'module_path' => drupal_get_path('module', 'my_module'),
      'resource_base' => $resource_url,
    ),
  ), array('type' => 'setting'));

  drupal_add_js($resource_url . '/js/my-script.jquery.min.js', array(
    'scope' => 'footer',
    'group' => JS_LIBRARY,
  ));
}