I have used Truecrypt for full system encryption on 2 laptops. I am very happy with that setup. Recently purchased desktop with RAID 1 setup - 2 hard drives using Intel Matrix Storage Technology and RAID controllers in Windows 7.
I would prefer to do full system encryption on the desktop computer but am not sure if this would work appropriately in RAID 1 protocol. In other words, not sure if the RAID functionality boots before Truecrypt (or perhaps some other challenge). As a backup plan, I could always mount a volume to store the most important files. Any input would be greatly appreciated.