encfs for the paranoid
EncFS is a free (GPL) FUSE-based cryptographic filesystem that transparently encrypts files, using an arbitrary directory as storage for the encrypted files (Wikipedia article).
One of the good things about encfs is that it allows you to keep your encrypted directory backed up on a removable disk or remote server, without having to decrypt and re-encrypt the data. And if you exclude the configuration file (that contains the key, which, in turn, is encrypted with a passphrase of your choice) from the backup, then you don’t have to worry about whether someone else could get a look at your backups — all they’d ever get is random gibberish.
The bad thing is that the config file normally sits within your encrypted directory. So if a Bad Guy manages to gain access to your primary disk (e.g. by stealing your laptop) and figure out your key-encryption passphrase, then you’re toast.
But encfs allows you to use an external program to get up to 2 KB worth of passphrase. So you could pick any nicely inconspicuous file (e.g. a photo of your cat) on your thumb drive, and mount your encrypted directory using a command line such as
encfs --extpass='cat /media/flashdisk/kitty.jpg | sha512sum' \<br /> /home/yourname/.secret /home/yourname/secret
Now your cat photo would serve as a key to your encrypted data, so you better make a couple of backup copies thereof (e.g. on Flickr where you could always re-download it when you happen to lose your original). Of course there’s another obvious problem: if the Bad Guys get your laptop they’d also get your .bash_history and might want to come back to steal [a copy of] your cat photo.
So you might want to modify your encfs command line to ask you for the key file without leaving any traces into your .bash_history.
encfs --extpass='cat `ssh-askpass` | sha512sum' \<br /> /home/yourname/.secret /home/yourname/secret
But of course if you’re dealing with Really Bаd Guys then you should keep in mind that a $5 wrench is a rather convincing argument.