Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in anyway.
Creating deployment documentation for .config file changes is a freek'n nightmare and something that should be automated as much as possible. I haven't found a tool that does this completely as I want but there's a number of XML Diff'ing tools around that do the hardest part of the job. I just found this one on MSDN. It's a little old now but it comes with source and it's fast and simple.
Ideally I'd like to be able to have XMLDoc comments in .config files and then generate some help from this - much like you can do with NDoc or Sandcastle for your code files.