Written by TMurgent's Tim Mangan, this book is the learning book for anyone that is repackaging applications into any format.

The book covers all of the fundamentals about what the installers are changing on the OS during installation and why.  It has been described as a reverse-engineering of the Windows API system.

It isn't free, but not that expensive either.  Available in paperback or eBook form from the TMurgent website here: The Application Book (tmurgent.com)