I've used Symantec's Ghost software in the past for cloning Windows based servers. It runs off a bootable CD and supports FAT, NTFS, EXT2 and EXT3 so it should do the job for Linux too.
Here's a link to the product page, I see they have a Trialware version available, but I'm not sure if it would be limited in some way.
http://www.symantec.com/en/za/ghost-solution-suite
Found this while searching for Ghost, and it may work for you too:
http://sourceforge.net/projects/g4l/
Good Luck!