I frequently use Panels for system and custom pages. In page.tpl.php, the whole Panels layout is dumped into the $content variable in the primary block region, which may not serve the needs of the design. My custom Panels layouts often built on the UI defined in page.tpl.php, so I like using an alternate template suggestion for those pages which has less structure, leaving Panels more freedom to take over the page completely.

<?php
/**
 * Implements theme_preprocess_page()
 */
function tsmithcreative_preprocess_page(&$variables) {
  // Call a stripped down "page--panel.tpl.php" when Panels
  // covers the entire layout. Otherwise, the standard
  // page.tpl.php contains the two column structure with
  // Drupal's block layout.
  $panel = panels_get_current_page_display();
  if ( isset($panel) && !empty($panel->layout) ) {
    $variables['theme_hook_suggestions'][] = 'page__panel';
  }
}

This can be a faster and lighter weight alternative to activating Panels-based overrides for all system pages or using a solution like Panels Everywhere.

The panels_get_current_page_display returns useful information about the Panels display as an object, including a layout property.

In template_preprocess_page, we can declare additional theme hook suggestions to use other templates. This example (in use on this site, actually) adds page--panel.tpl.php for any Panels layout, but could easily be adapted for conditional templates based on layout.