Skype version 6.16 has now been released and if you would like to either add this to your Configuration Manager Software Catalog or even have it available through WDS or Group Policy, then you will want to download the MSI file for it.
If you want to distribute Skype as a silent install, then you can use the code as below:
WDS or Group Policy
SkypeSetup.msi /q /norestart
msiexec /i "SkypeSetup.msi" /q /norestart