Emco MSI Package Builder software
This is dredging up an old post and I'm sure you have found alternate solutions. However, if you are still looking for a slick way to deal with deploying software that only come with exe installers then you may want to check out Emco MSI Package Builder. I've been using this software for over a year now and very much recommend it. The license is decently priced (we have the enterpise version) and the software works well. I've deploy 30-40 packages with it, most with very little difficulty.
Originally Posted by Little-Miss
This software basically monitors your installation process onto an existing machine and then packages it into a msi. I then use GPOs to deploy the msi. I have used this for everything from .exe installers to drag and drop installers (manually creating menu shortcuts, etc.).
Generally I avoid startup scripts for installation except for packages that pretty much well demand it (I'm looking at you MS Office and Visual Studio).