[eluser]Colin Williams[/eluser]
You could always use symlinks
Code:
ln -s /path/to/site1/app/controllers/example.php /path/to/site2/app/controllers/example.php
And it doesn't have to be a nightmare to have two separate instances of the same controller or model. Just maintain one "core" version and push it out to all apps/sites when it's updated and is stable.