Adding Custom JS to CKEditor I'm looking for a way to add custom JS to the CKEditor instance that is being created by the WYSIWYG module.

I posted a feature request on the WYSIWYG module's issue que, but sun suggested I post here as well. http://drupal.org/node/1126656

If you're wondering about why I want to add custom JS, the reason is so that I can adjust WYSIWYG input to more accurately reflect the WYSIWYG output.
You can edit/add CKEditor settings by implementing hook_wysiwyg_editor_settings_alter(), see Allow configuration of advanced editor settings - comment #52 and later comments for examples.

If you want your own script to run after CKEditor has loaded, maybe How to attach Javascript to a form so that it loads AFTER CKEditor can help you.