It would be really sweet to have a wysiwyg editor where the output is in markdown syntax instead of HTML. This would be a nice combo with e.g. Drupal input formats.
And probably the other direction exists as well.
So, the thing to do here would be to plug a two-directional filter between the original text area and the wysiwyg.
I have not studied the API of CKEditor yet, so I thought I start with a request in the forum :)