I think the best nursery man and the best potter in America do the greatest job I have seen.
The best shipping box job I have seen for live trees is from Evergreengardenworks.com, I think they have a write up on their method at the website.
For shipping pots WildThings bonsai does a very good job, when they do not have a professional service pack them he uses lots of spongey carpet pad to wrap the pots very well and to fill the box in tight. I think this method might have a chance in passing the old "drop an egg off a rooftop with out it cracking" test from science class.
Copy these two sellers methods and you won't be running into problems.