My first thought was that you could hide much of the existence of such a system with a collection of a couple existing tools:
<A HREF="http://www.colinux.org/">CoLinux</A> to run a Linux distro *under* Windows. Boot the computer all you want, it's running Windows...
<A HREF="http://www.truecrypt.org/">TrueCruypt</A> has all kinds of ways of hiding the existence of an encrypted volume: outright steganography, plausible deniability, the ability to mount a file (such as a file that looks like a Debian install DVD or the latest Hollywood blockbuster), etc.
So, at this point you have a hidden, encrypted Linux operating system that you run directly under Windows, so that, from the outside, the computer looks perfectly normal. This doesn't help with the chaff, but it's a start.