I guess I am looking for some generic information of how individual packages install/uninstall them self.
The reason I need to do it manually is because I have a personalized cygwin version and don't want to be forced to upgrade. The version I have now is with me for many years and works great in XP, with these small improvements I put into it once a while, which I don't want to miss after an upgrade.
Currently, I want to manually uninstall the following packages (and possibly other packages if left redundant after uninstallation)
emacs-21.2 ruby 1.8
Both of the above were coming with the old setup.exe. For emacs, I found I never used it in windows platform. For ruby, I upgraded to 1.9.1 by compiling the source code.