This tutorial will demonstrate how to encrypt an entire partition on a hard drive.  You can use this to encrypt an entire drive, or a particular partition.  I use the Ubuntu Linux version of Truecrypt in this tutorial.  Depending on your operating system, you could have different options to choose from when it comes to encryption and whether or not you can encrypt a system drive.  The majority of the software is the same across all operating systems.  Compared to other encrypting software available in Ubuntu, or even Linux in general, Truecrypt is the most user friendly.