Let's say your Windows System Partition is encrypted using TrueCrypt. Then you run Ubuntu via a USB Stick. I understand that it is possible to mount a TrueCrypt encrypted partition on Linux, but is there anything stopping you from doing this to a TrueCrypt encrypted Windows System Partition?
The Truecrypt FAQ states:
Will I be able to mount my TrueCrypt volume (container) on any computer?
Yes, TrueCrypt volumes are independent of the operating system. You will be able to mount your TrueCrypt volume on any computer on which you can run TrueCrypt (see also the question 'Can I use TrueCrypt on Windows if I do not have administrator privileges?').
There is nothing obviously special about a system partition compared to other truecrypt volume types. That said, I have not done this personally. Caveat emptor.