Hey there,
I've been through this situation before, so hopefully I can be of help.
When I went home from college over winter break, I simply couldn't fly home my entire system in its Antec P160 case -- so instead I just brought my 160GB hard drive home so I could still access my media.
The hard drive originally came in this shiny, translucent, dark grey plastic; I just put the drive back into that bag, gave it a few layers of bubble wrap, and put it into my carry-on backpack. There were no hassles whatsoever. My hard drive works fine after two such trips.
X-ray scanners shouldn't affect hard disks -- think of all the iPods that get sent through airport scanners everyday.