Skype has always offered a business version of their installer in MSI format. It can be found here. Facebook chat integration is missing in the business version, though. There is a regular offline installer in EXE format, but it can’t be extracted to get the MSI file to modify it.
They previously had one, but it’s nowhere to be found on their website for the past few versions. A few months ago I found a link to the normal MSI installer with Facebook chat integration, which is the one I modify to make my custom installers.
You can use this link to download it:
http://download.skype.com/msi/SkypeSetup_6.7.0.102.msi
Take into account that you will need to change the version number each time a new one is available.