First you'll need to download Business version of Skype, SkypeSetup.msi from http://www.skype.com/intl/en-gb/business/download and rest is easy as deploying standard MSI file,
You can also modify it with Orca or create a new transform, for example you might want to remove
Desktop Shortcut : Shortcut\SkypeDesktopShortcut
Sent to : Shortcut\SkypeSentToShortcut
Start after Install : CustomAction\SkypeStart1
Start at Windows Start up : Registry\reg08D3E7E5CD85CB55680CCDE42A2E2625 (Software\Microsoft\Windows\CurrentVersion\Run)
and run with the new mst, e.g. msiexec /i SkypeSetup.msi Transforms=SkypeCustom.mst ALLUSERS=1 /qb
Also I recommend you to download Skype IT Admin Guide from http://download.skype.com/share/business/guides/skype-it-administrators-guide.pdf
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