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.

This post http://www.debianadmin.com/filesystem-encryption-tools-for-l... has a fairly good introduction to the most popular flavours. It's going to vary depending on your needs.