http://www.truecrypt.org/faq.php

Q: Can TrueCrypt encrypt a Windows boot partition?

A: TrueCrypt 5.0 (to be released in February 2008) will support encryption of a Windows boot partition/drive. In the meantime, TrueCrypt can encrypt (on-the-fly) a disk image containing an installed operating system that you run (boot) under virtual-machine software, such as Virtual PC, VirtualBox, or VMware (VirtualBox OSE is free and open-source; Virtual PC and some editions of VMware are free).

Tip: That way, you can have Windows installed in a hidden volume.