I have released a script, vmclone.pl, to assist in the cloning of full Virtual Machines within an ESX Server box. This came about because of a gap in functionality between replicating individual hard disks and the clone option in the VI client that was mostly missing from VMs.
The tool will replicate and rename all the files in a VM with a single command line execution and optionally allows you to tweak (using regex) some of the options such as changing the memory size of a VM.
The tool is available here: http://www.pgregg.com/projects/vmclone/
I would appreciate any feedback or suggestions on it.