The latest APM planner has full pid/planner/gcs while under hil/real using mavlink. Some new features since the last major release are a
Planning via Xbee
HIL via Xbee if you so wish
And the ability to do all the above all at once.
This latest version can be download from the SVN at http://code.google.com/p/ardupilot-mega/source/browse/Tools/trunk/A... OR by using the Update feature in the menu.