With Truecrypt, you can encrypt the whole system partition, I guess that goes for USB sticks too. The bootloader will decrypt the whole USB partition after you supply it with the correct password.

For extra extra security, you could even have a Truecrypt file container inside the whole USB partition container, with perhaps a dummy wallet as a hidden volume, so if you are forced to open your wallet, you can just type the alternate password and then your alternate wallet with perhaps only a few coins will decrypt.