TrueCrypt supports encrypting a system partition while operating system is running.
From the docs:
Note that TrueCrypt can encrypt an existing unencrypted system partition/drive in-place while the operating system is running (while the system is being encrypted, you can use your computer as usual without any restrictions). Likewise, a TrueCrypt-encrypted system partition/drive can be decrypted in-place while the operating system is running. You can interrupt the process of encryption or decryption anytime, leave the partition/drive partially unencrypted, restart or shut down the computer, and then resume the process, which will continue from the point it was stopped.
The question is. How is it implemented? How does TrueCrypt keep one part of the partition encrypted and the other non-encrypted? And how does it provide access to both parts while constantly encrypting the unencrypted one? What happens if the systems tries to access the data (or even write it) which is being encrypted at the moment (transferred from non-encrypted section of the partition into encrypted)?