Have you heard of WinBatch?
I picked it up a couple years ago to do some real basic scripting and batch writing for some of my packages. It has a Compiler that converts the batch file into .exe file and give it any name you like. You can put all kinds of info into the file header, including date, name, comments, even your name and department. Once I have compiled the file, I just add it to my package and have it install to the C:\Windows folder. (that way normal users w/out admin rights can't delete it).
When I need to find out who has what app and what version, I use SMS Web Reports to query the network for the file.
WinBatch is comparitively cheap to get (I think I paid a couple hundred for the Compiler license) and is a pretty versatile tool for all kinds of stuff.
You can get the batch program for free at
www.WinBatch.com, but you have to pay for the Compiler. It's worth downloading and at least checking out.