I think "cloning" refers to any process that moves the actual bit patterns--rather than depending on a file system. If you copy a file, you don't get any information on the file **system**, partitions, boot code, etc.
Norton ghost is a popular cloning program for Windows. The Linux equivalent is dd.
dd if=/dev/hda........clones an entire drive, including the first 63 sectors (sector 0 being the mbr)
dd if=/dev/hda1.......clones only the first partition on hda
you can "clone" to an image, or to another raw device. An image is a file which lives within your filesystem, whereas cloning to a raw device will not depend on any filesystem.
For a fantastic tutorial on dd, search here for a thread called "learn the dd command" by Awesome Machine.