CKEditor custom configuration (implemented using WYSIWYG module)
Look at hook_wysiwyg_settings_alter


  Act on editor profile settings.
  
  This hook is invoked from wysiwyg_get_editor_config() after the
  JavaScript settings have been generated for an editor profile and
  before the settings are added to the page. The settings may be
  customized or enhanced; typically with options that cannot be
  controlled through Wysiwyg module's administrative UI currently.
  
  Modules implementing this hook to enforce settings that can also be
  controlled through the UI should also implement
  hook_form_wysiwyg_profile_form_alter() to adjust or at least indicate
  on the editor profile configuration form that certain/affected
  settings cannot be changed.


Additionally this blog post by Fuse Interactive: WYSIWYG MODULE + CKEDITOR: TAMING THE BEAST goes into great depths on how to make use of this hook. From the blog post ...

/**
 * Implements hook_wysiwyg_editor_settings_alter()
 */
function ckeditor_custom_wysiwyg_editor_settings_alter(&amp;$settings, $context) {

  // The $context variable contains information about the wysiwyg profile we're using
  // In this case we just need to check that the editor being used is ckeditor

  if ($context['profile']-&gt;editor == 'ckeditor') {

    // The $settings variable contains all the config options ckeditor uses. 
    // The array keys correspond directly with any setting that can be applied 
    // to CKEditor - as outlined in the CKEditor docs: 
    // http://docs.cksource.com/ckeditor_api/symbols/CKEDITOR.config.html 
    // Another way to override configuration is to use your own configuration javascript
    // file. In this case, we're going to add our own configuration file that will
    // Hold our stylesSet customizations... 
    $settings['customConfig'] = base_path() . drupal_get_path('module', 'ckeditor_custom') .
                                '/ckeditor_custom_config.js';

    // We are also going to specify a custom body id and class
    $settings['bodyId'] = 'ckeditor_custom_id';
    $settings['bodyClass'] = 'ckeditor_custom_class';

    // To see what's in $settings and $context, install the devel module 
    // And run the variables through the dpm() function. 
  }
}