I've always been fond of storing a directory structure encrypted in a file (ala TrueCrypt or PGPDisk). I borrowed instructions from here.

Create the raw file to contain your encrypted data.

dd if=/dev/urandom of=~/encrypted.bin bs=1M count=100 Find the next available loop device and map this file to it. losetup -f losetup /dev/loop0 ~/encrypted.bin
Setup the crypto filesystem, open it with the correct password, format the partition ext3, and finally mount the newly created filesystem as /mnt/tmp

cryptsetup --verbose --cipher "aes-cbc-essiv:sha256" --key-size 256 --verify-passphrase luksFormat /dev/loop0 cryptsetup luksOpen /dev/loop0 my-crypt mkfs.ext3 /dev/mapper/my-crypt mount -t ext3 -o rw,defaults /dev/mapper/my-crypt /mnt/tmp/
When you're all done, and want to secure all the files do the following. Umount the filesystem, close the crypto link, remove the file to loopback device link.

umount /mnt/tmp/ cryptsetup luksClose my-crypt losetup -d /dev/loop0