Thank you for the interesting article! I'm just starting to try and get real virtualization going as a development environment and have run into similar issues, too. Since we're still "trying out" utilizing VMs to develop and test things, we also are working against a very limited budget. I.e., VMware Server (free), old retired server hardware (CPU, RAM, and disk storage definitely limit what all we can do), and then trying to get everyone on the same page.
It would be nice if there was a better (free) way to manage everything, too....as we don't have the resources now to go with one of the relatively expensive management tools.
Either way, it's a good learning experience and we're starting to see how powerful it can be. Thanks for the idea of versioning the VMs with source code software, too!