If you're checking it in put it in the original box for best protection. Of course every idiot out there will know you're bringing back a Mac Pro but then again it's too big to be stolen (maybe?).

Warranty is important, I've done my fair share of long distance flights with computers in checked in luggage but once I had my then almost new Powermac 6100 die on me, I checked it in my bag, with enough padding etc. But once home it died, no power, no nothing. I think it may have been some sort of static problem but I can't be sure. Fortunately it was replaced under warranty.

I've brought two notebooks with me, one personal and one business during my travels to Europe and the US before. It's a lot more hassle since security requires all notebooks to be out of the bag for scanning but no questions asked.