Using DESlock+ Folder Encryption, almost any folder on the system can be encrypted. Some system folders cannot be encrypted, these are:

C:\Windows 

C:\Program Files

C:\Program Files (x86)  (64bit systems only)

C:\Documents and Settings  (Windows XP)

C:\Users  (Windows Vista or later)

However, you can encrypt folders on the Desktop and 'My Documents', but only if you're not using a temporary or roaming profile.