Even with a fully encrypted system (root and swap partitions), your data is still vulnerable while your computer is on. That's why Bruce Schneier recommends a two-tier encryption strategy.

The idea is that infrequently used files are moved to a separate partition, encrypted with a different key. That way, the bulk of your data files is protected even if your laptop is hijacked or if an intruder manages to steal some files while your main partition is decrypted.

On Debian and Ubuntu, a secure archive area can be created easily using an encrypted loopback partition and the cryptmount package.

Add this to /etc/cryptmount/cmtab:

archives {
    dev=/home/username/.archives
    dir=/home/username/archives
    fstype=ext3 fsoptions=defaults cipher=aes

    keyfile=/home/username/.archives.key
    keyhash=sha1 keycipher=des3
}

Create the key and the 512 MB loopback partition:

sudo cryptmount --generate-key 32 archives
dd if=/dev/zero of=.archives bs=1M count=512
mkdir archives
sudo cryptmount --prepare archives
sudo mkfs.ext3 -m 0 /dev/mapper/archives
sudo cryptmount --release archives

Fix the permissions so that you can write to this partition with your normal user account:

cryptmount archives
cd archives
sudo chown username:username
cryptmount -u archives

Then you can mount and umount that partition using:

cryptmount archives

and

cryptmount -u archives