Question: I'm looking at deploying some software via GPSI and the current version of the software is distributed as a .exe so I need to convert it to an MSI file.

furthermore, why does MS still distribute some of its software (WMI Tools) as .exe

Answer: 
Heh, I'll try and answer my own question..
I'm also going to look at The [AppDeploy Repackager](http://www.appdeploy.com/tools/repackager/). It looks like it will do pretty much the same thing as Joseph mentioned. I'll see which one does the job with less stress on my part :)
[Microsoft's Windows Installer XML toolkit](http://wix.sourceforge.net/) (WiX).