In the past a lot of people would extract the underlying MSI from the executable to install it that way. However I’ve tested it using a few of their switches, some cursory Googling helped me find some commands that would perform the tasks I wanted.  For some reason just uploading the executable and specifying the switches didn’t work. So instead I created an install.bat, which is better anyways because it will now check for Skype being installed prior to installation. This will silently install just the program, and won't launch it after the install, and make sure to not restart the machine. The install.bat is located under scripts.

1.       Zip the executable and install.bat together

2.       Upload into KACE. Check Don’t prepend with MSIEXEC.exe and delete downloaded files.

Install.bat

if exist "C:\Program Files\Skype" goto END

if exist "C:\Program Files(x86)\Skype" goto END

SkypeSetupFull.exe /verysilent /norestart /nolaunch

:END

It is very difficult to disable skype updates. So I have written a blog post to give everyone here direction on how to do it in package. Read my blog post here:

http://msiworld.blogspot.com.au/2013/05/packaging-skype-with-auto-update.html

This was posted under Skype 5 so i copied and pasted here after making a new tag.  Thanks to user Starzinger for the great post !

This is for Skype 6.0 Business

In my case, i wanted the package to:

*Install silentlly
*Disable Skypes auto update check/Check for newer versions
*Remove the icon from the desktop
*Disable Skype from starting automaticlly after deployment/computer reboot
*Install for All Users

First, download the business version and save the SkypeSetup.msi file in a folder named Skype for example.

http://www.skype.com/intl/sv/business/download/ For Swedish OR 
http://www.skype.com/intl/en-us/business/download/ for US version

Extract the .msi with 7-zip.

Create a .bat file named installSkype.bat within the Skype folder and paste the following:

msiexec.exe /i skypesetup.msi /qn STARTSKYPE=FALSE SKYPEREMOVAL=DEFAULT ALLUSERS=1 TRANSFORMS=:RemoveDesktopShortcut.mst
regedit.exe /S Skype.reg

Then create a .reg file named Skype.reg and paste the following:

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Skype\Phone]
"DisableVersionCheck"=dword:00000001

Run installSkype.bat ( as Administrator )

Done!

More info/registry settings, for example disable file transfer etc. Check out Skypes administrators guide, as mentioned before:
https://support.skype.com/resources/sites/SKYPE/content/live/DOCUMENTS/0/DO5/en_US/skype-it-administrators-guide.pdf

-Dave Hope has a couple of customized .mst´s if you want to use them instead for some reason.

Go to http://davehope.co.uk/Blog/skype-transform-deploying-skype/ and download the desired .mst file to the Skype folder.
For example http://davehope.co.uk/Projects/MST-Skype51.mst

Then modify the .bat file, like this:

msiexec.exe /i skypesetup.msi /qn STARTSKYPE=FALSE SKYPEREMOVAL=DEFAULT ALLUSERS=1 TRANSFORMS=:MST-Skype51.mst
regedit.exe /S Skype.reg

Good luck!

The .msi of Skype v6.11 was super easy to push out with my K1000:

1.  Download the MSI installer from Skype's website:  http://www.skype.com/en/business/downloading/

2.  For distribution via K1000:

    Installation command:  Use default
    Run Parameters:  /qn /i
    Delete Downloaded files - checked 

That's it!  While researching, I also found the following business guide.  While a couple of years old, it may have some useful information:  http://download.skype.com/share/business/guides/skype-it-administrators-guide.pdf

I found this solution to disable autoupdate for Skype 6.x. You must change on registry: 

HKLM\Software\WOW6432Node\Skype\Installer

(Dword value) "InstallUpdates"    value: 0

I got tired of the clustershot way that Skype puts all its deployment features. I created an transform that.

1) - Kills the desktop shortcut

2) - Kills autorun

3) - Kills autoupdate

I tend to apply my transforms to my .msi's in order to reduce complexity. So here's the msi switches I use on top. Stops Skype from opening after install, removes previous versions, and installs for All Users rather than the logged on user. Obviously to use the Transform rather than apply it, just add the transform switch as well.

msiexec.exe /i skypesetup.msi /qn STARTSKYPE=FALSE SKYPEREMOVAL=DEFAULT ALLUSERS=1

Transform file:

https://skydrive.live.com/redir?resid=5CD044B32EBE8AB9!409&authkey=!AHCLX13zpeXG9Ng

Hope it helps