Django upgrading to 1.9 error "AppRegistryNotReady: Apps aren't loaded yet."
Try to add this lines to the top of your settings file:
import django
django.setup()
And if this will not help you try to remove third-party applications from your installed apps list one-by-one.
I'd a custom function written on one of my models __init__.py file. It was causing the error. When I moved this function from __init__.py it worked.