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When it comes to virtual desktop infrastructure, administrators have a lot of choices. You may have wondered about the differences between VDI software options, remote display protocols or all the licenses out there. In this series, we tackle some of the biggest head-scratchers facing VDI admins to help you get things straight.

There are so many application virtualization tools out there, you need to know how to tell them apart.

Application virtualization separates the app from the OS, allowing IT to deliver applications in the most efficient way possible. These are just a few of the other benefits: You don't have to install apps. They are easier to patch and upgrade. And you can run multiple versions on the same OS. Plus, in the age of bring your own device, application streaming allows IT to deliver apps to many kinds of endpoints.

Some of the major application delivery tools are VMware ThinApp, Citrix Systems XenApp and Microsoft App-V. Of course, each product integrates best with its own vendor's offerings, so if you run VMware View, for instance, ThinApp might be your top choice.

In this application virtualization comparison, we break down the different features, capabilities and support these tools offer. Let's get this straight:

Citrix XenApp

ThinApp and App-V only provide app virtualization, but XenApp is an overall application delivery system. Citrix Streaming, which you can get a license for through XenApp or XenDesktop, is the vendor's application virtualization technology.

XenApp is pretty much confined to its own environment or a XenClient environment, making it difficult to port around. Still, Citrix added support for Microsoft App-V in XenApp 6.0. At Citrix Synergy 2012, the company combined XenApp with its desktop virtualization product, XenDesktop, into the Excalibur offering.

XenApp is useful for IT shops that have a wide variety of applications -- old and new -- and want to virtualize apps with Citrix Streaming that ThinApp and App-V don't support.

What's new in Citrix XenApp 6.5?
Citrix XenApp 6.5 reduces application launch times through the Instant App Access feature. Improvements to the HDX protocol also allow apps to be run in higher-latency environments. Plus, XenApp 6.5 includes a Mobility Pack that improves application delivery to mobile devices.

What you need to know about migrating to XenApp 6.5
IT shops have very little time to migrate from XenApp 4.5, 5.0 or 6.0 to the latest version. Support for XenApp 4.5 ends on March 31, 2013, and support for version 6.0 ends on July 15th, 2013, only three months later. Since XenApp is based on Remote Desktop Session Host, admins also need to be aware of Windows Server end-of-life dates. Not all applications are compatible with all Windows Server versions, either.

These caveats make things especially difficult when licensing and running XenApp and Citrix Streaming compared to other application virtualization tools.

VMware ThinApp

VMware ThinApp offers a few capabilities that XenApp and App-V do not. For instance, it can deliver offline applications, and it's the most portable of the application virtualization tools. You can run ThinApp applications from almost anywhere because users don't need to install software or device drivers. Plus, they don't need admin rights to access applications from remote locations, such as an airport lounge.

Still, some administrators say VMware ThinApp is more cumbersome to deploy. It's also trickier to manage applications because it doesn't come with a centralized management platform. If you're experimenting with the cloud and mobility, you should also know that ThinApp 4.7 integrates with VMware's Horizon Application Manager.

Everything you need to know about VMware ThinApp
VMware ThinApp 4.6 integrates with View 4.5 and above, but not all administrators need to deliver virtualized applications to virtual desktops. There's a lot to know about how to license, manage and deploy ThinApps -- particularly if you're using them in a View environment.

ThinApp Factory mass-produces virtualized apps
A new endeavor by VMware, ThinApp Factory automates the application packaging process. This virtual appliance, which plugs into vCenter or VMware Workstation, takes the encoding and distribution out of administrators' hands.

Microsoft App-V

App-V provides centralized management, so admins can limit users' access to certain apps. Microsoft's application virtualization tool is popular in shops moving to Windows 7 or 8 because it lets users interact with virtualized Windows apps, such as Office. The latest version, App-V 5.0, reduces disk requirements by allowing IT to turn off local application storage. Plus, it has enhanced application diagnostics and monitoring.

VMware user votes for App-V
Although admins like ThinApp's ability to install without an agent, there are some upsides to using an agent-based approach. App-V has an agent component that pushes applications to the user without Active Directory settings, using Microsoft System Center Configuration Manager. This application virtualization tool also allows you to break down application suites (such as Office) and deliver the apps without losing any integration functionality.

What's new in Microsoft App-V 5.0
The latest version of App-V provides a more native application experience to users. IT can also deploy and track apps through Microsoft Silverlight, which means they can access their admin console on the Internet. For mobile workers, App-V 5.0 allows applications to stream over a WAN using Direct Access, and it also integrates with Windows To Go.

Choosing an application virtualization tool

Once you've reviewed the options, you're ready to pick an application virtualization tool. Just remember, the major vendors aren't the only choices.

Citrix, VMware, Microsoft compete for app virtualization dominance
Each of these application virtualization tools has its pros and cons, and the gap between them is closing. VMware in particular has a tough road to travel because Citrix and Microsoft are close partners. ThinApp has portability in its pocket, but App-V supports 64-bit and server applications, which ThinApp does not.

Alternatives to the major vendors
Don't forget that ThinApp, XenApp and App-V aren't the only options; there are other applications virtualization tools out there. For instance, Spoon Studio is easy to use and integrates with the company's cloud offering. InstallFree is another choice, but it doesn't offer offline functionality.

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