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 ;)
I copy here two lists from a couple of webpages I found.

A long list of deployment software, including repackagers, with descriptions added: <http://www.installsite.org/pages/en/tt_corp.htm>

Here I copy only the names mentioned in this webpage:

* AdminStudio
* Advanced Installer Architect
* AppDeploy Repackager
* Asdis
* CapaInstaller ezMSI
* BMC Software
* MSI Package Builder
* NetInstall
* Network Software Scanner
* Packaging Robot
* Prism
* Radia
* RayPack
* Real Packaging
* RemoteExec
* Remote Installer
* Smart Packager

One more list from: <http://www.interfacett.com/blogs/exe-msi-deploy-exe-based-installer-microsoft-world/>

Probably not all of them are repackagers.

* WinInstall
* wItem Installer (also called Installer2Go)
* VMWare ThinApp
* EXE to MSI Converter (exetomsi.com)
* AppDeploy repackager
* Exemsi MSI Wrapper (exemsi.com)
* Advanced Installer (advancedinstaller.com)