I had thought of HD encryption, but I don't like solutions that leave part of the drive unencrypted. My desktop system at home has an add-on interface card that requires a USB "key" (key in the literal sense, it's got a 2048-bit random noise key hard-coded into it) in order to activate the card and decrypt the data on the drive. Everything is encrypted...the entire OS and all data. Everything flows through the encryption system. I'm looking for something similar for a laptop.
Unfortunately, it also occurs to me that should we reach the point where battery-powered items are required to be checked, it will probably also be next to impossible to carry-on a USB key/drive. Too hard to prove it's inert/too easy to convert it into a triggering device (if you had such motivations). Which puts me in the same predicament...data that shouldn't leave my sight (encrypted or not) is now in the cargo hold of the plane, being handled by people I can't see and don't know.
The more I think about it, the more I realize that any such policy would end up being an unmitigated disaster from a data security perspective.