In our session on TechED 2014, Configuration Manager 2012 Community Jewels in Houston we did a demo of Application Importer by Mattias Benninge.
The tool saves a lot of time and makes it really easy to import an .MSI application as it will do everything for you, create Collection, create AD group, Create query for the AD group, distribute the content, deploy the application, basically everything you need to do to deploy and application.
Basically you can import the .MSI and then add a computer or user depending on how you deploy your applications to the AD group and it will deploy to the client.
During our session there was a little bug in the tool but that has now been sorted out in version 0.3.
I recommend that you download it and try it out: https://sccmappimp.codeplex.com/
Great work Mattias!