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A new complexity layer: Most Windows apps were not developed to run in a virtual environment. This might cause unforeseen problems. Whenever problems occur, you will wonder whether the app itself or the virtualized environment is the cause.
Vendor might deny support: If you tell your vendor that you are running their application in a virtual environment, they might deny support.
Problematic apps: Some apps, especially those installing their own system drivers, don't work as virtualized applications. Note that there are differences between the different application virtualization solutions here. Some are more robust than others.
Shell integration: One reason that applications are installed is because they have to be integrated in the Windows shell. Since virtualized apps are not installed on the host, shell integration has to be established by other means. All virtualization products offer solutions for this problem, but it usually means extra work. How much extra time you to have to invest in this depends on the product and the application.
More work for you: Application virtualization can simplify many admin tasks. However, it is a new technology which you have to learn first. Complex virtualization solutions require a lot of preparation in advance. If you can't give up your current software deployment solution, it will mean extra work for you.
Changes to your infrastructure: Many things work differently with virtualized apps. For example, you might not be able to use your current patch management solution anymore.
Single point of failure: Launching apps from a server has its advantages, but network outages or server problems increase the risk of system-wide failures. You can usually copy virtualized apps to the desktops, but then you give away one of the benefits of software virtualization.
Bandwidth requirements: Streaming apps to end users is an interesting technology. You just have to make sure that you always have the necessary bandwidth available.
Costs: Prices of application virtualization solutions range from $30 to $100 per client.
The importance of each point depends heavily on your environment. Hence, just one of the disadvantages might be a knockdown argument for you. Of course, various application virtualization solutions also differ in the way they deal with the disadvantages listed here. Even though I see the risks of this relatively new technology, I can imagine introducing software virtualization in my organization. In my opinion, the biggest downside is the cost. At the moment, I don't see how we could give up our current software deployment solution (SMS) which would mean additional costs for us.
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In the next two posts in this series I will discuss the features and the differences between application virtualization products.