When you talk with folks in an IT shop running virtualization in their environment, one of the common complaints heard is that ISVs don't always "officially support" their own applications running inside a virtual machine. And if you choose to virtualize those application anyway and a problem arises -- well, you could be on your own.
If there is no official support from the ISV for running the application on a virtualization platform and a problem does arise, the ISV typically requires you to then reproduce the problem on a physical machine. Hey, no problem, right? After all, what administrator doesn't have all the spare time in the world to build out an exact replica of the guest environment on to a physical machine just to prove a point?
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In some cases, administrators got wise to the game and started leaving out the small detail about how the application is installed inside of a virtual machine. This usually works when support is over the phone and not in person. And hopefully the question about virtualization either never comes up or it comes up too far down the support path, once a resolution to the problem comes about.
Luckily, things are changing. We are no longer in the virtualization dark ages where VMs were considered black magic and something ISVs refused to acknowledge as viable platforms. But things still aren't perfect even in this virtualization period of enlightenment of 2009. Many ISVs may go beyond just acknowledging virtualization and actually use it within their own walls for development, testing, or production use. But they may still be falling short of including it in their own official support agreement with customers.