Another suggestion:
While it may sound paranoid and I know how to use TrueCrypt and FileVault, it would be an nice feature to enable password encryption for projects (like password protected documents in OpenOffice or word). Just makes it easier to carry projects around on an unencrypted USB stick, for example.
There wouldn’t be much point in password protecting a .scriv file given that it is really just a folder of files. If you moved it to a computer without Scrivener on it, a .scriv file would just look like a regular folder (as it will on Windows). And even with a computer that has Scrivener on it, you can access the files inside using Show Package Contents via the Finder.
Best,
Keith
P.S. I’ve moved this thread to the Wish List section.
For thumb drives, I recommend creating encrypted disk images using Disk Utility. Unlike FileVault, they can be carried around from computer to computer just like any other DMG. The only difference is that they require a password to mount, and the contents are scrambled with a fairly strong method of encryption—certainly enough to foil the average person that picks up your dropped USB drive.