Figured I should share my two favorite applications I use frequently for repackaging setup files to .Msi files for integration into MDT or SCCM. Best part is they are both FREE.
AdminStudio Configuration Manager Edition
Latest Version: 9.5
Developed by Flexera, approved by Microsoft and integrated into SCCM. Highly tested and simple. one of the largest Cons, is that the free version requires a SCCM server for usage.
Note: Registration on FlexeraSoftware.com to obtain license key.
The AppDeploy Repackager
Latest Version: 1.2
Deployed by Team at Appdeploy.com, which was recently purchased by Dell. To my satisfaction and many others, Dell still provides this resource for free. Very simple to use, however, not well tested in ECCM installations.