DiskCryptor is an open-source tool which makes it easy to encrypt any or all of your disk partitions, including the system drive.
To use the program you have to do little more than select a drive and encryption algorithm (AES-256, Twofish and Serpent are supported). DiskCryptor will then encrypt the drive according to your passphrase, and in future only someone who knows this will be able to access your files.
This should also apply to system and bootable partitions, too, as the program offers pre-boot authentication, strong compatibility with third party boot loaders, and more.
However, as the latest DiskCryptor download is more than a year old (and even that's a beta) the idea of using it to encrypt a system drive makes us a little nervous - the consequences of some previously unnoticed bug would just be too serious. (And it didn't help that we found the program crashed a couple of times for no apparent reason.)
Unless you're brave or fully backed up, then, you might prefer to use the program to protect only external storage devices. It can create encrypted CDs, DVDs and USB flash drives with the absolute minimum of hassle, perfect if you need to transport sensitive or confidential files.