There are actually several ways to do this I use encfs which uses FUSE to mount an encrypted directory as another directory, the advantages are that it works in userland and it's braindead simple. I wouldn't want to run a database off of it, but for a bunch of text files it's perfectly adequate. A lot of people are fans of truecrypt and if you are seriously concerned about devoted efforts to get at high-value data you probably want to just encrypt the disk partition you are using.
Thanks for the article, there is lots of great info on there. I need to figure something out where I can make secure backups to some remote server. I guess there is no real perfect solution, but TrueCrypt looks good. I ran across this one talking about some deeper security constraints with this that I think offers a nice insight. http://www.schneier.com/blog/archives/2008/07/truecrypts_den...