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: 
IMO WiX may be the best way, since repackager working with snapshots tend to record unrelated changes, as far as you don't spend some time setting exclusions...

Using the [Wixtool](http://sourceforge.net/projects/wixtool/) makes the creation of an MSI quite convenient instead of writing lots of xml containers ;)
[Microsoft's Windows Installer XML toolkit](http://wix.sourceforge.net/) (WiX).