One of the biggest issues with Truecrypt 5.0’s System Partition encryption was that it couldn’t hibernate the OS; which was holding me back from deploying it company-wide. Thankfully, this is now fixed in 5.1 🙂
Support for hibernation on computers where the system partition is encrypted (previous versions of TrueCrypt prevented the system from hibernating when the system partition was encrypted). (Windows Vista/XP/2008/2003)
Other things of note include faster encryption/decryption using AES, and faster boot times.