I have a large number of Applications that each need multiple steps, such as Run this exe and then run msiexec.exe.  What is the best way to accomplish this?

There is a Powershell Application Deployment Toolkit, as anyone used this?  

The requirement would be wait for the exe to complete prior to running msiexec.exe.

Either user Powershell Application Deployment Toolkit, a simple batch, dependencies or whatever fits best. There is no one-fits-all answer here.