The Solution to my problem is to simply let my plugins output run through the do_shortcode()
-Function of WordPress as pointed out by this article: Using Shortcodes Everywhere
I updated my plugin so it uses shortcodes, too, so now my output looks like this:
// Add this upon plugin initialization
add_shortcode( 'dosomethingawesome', array( &$this, 'output_callback') );
/**
* Plugins output
*
* Fetches the output from handle_callback() and then runs it through the
* do_shortcode() function to work with other plugins, too
*
* @uses do_shortcode()
* @access public
* @return string
*/
// {{{ output_callback()
public function output_callback() {
$sOutput = $this->handle_callback(); //returns the string of my plugins action
return do_shortcode($sOutput);
}
// }}}