A while ago I wrote about how to put your OS X Mail into an encrypted drive image. However, I've noticed that drive images don't get indexed by Spotlight by default - so you can't do searches on message contents any more.
You can fix this by opening up the Terminal and typing:
mdutil -i on /Volumes/Mail
If you're not running as the admin user (another good security idea), you'll need to switch to your user access and/or run this with 'sudo' as well.