I just noticed this excellent guide on deploying ThinApp. I would suggest that anyone that wants to start using ThinApp looks into this guide, I guess it could be considered as a “mini-course” on howto ThinApp an application:

This document provides guidance for customers seeking to package and deploy applications efficiently with VMware ThinApp. It addresses most relevant deployment considerations but does not provide comprehensive detail. Please see the VMware ThinApp User’s Manual for the specifics of implementation and further explanation.