Creating a self-extracting .exe that installs parts of Cygwin is not a very Cygwin-friendly way of distributing software, as it won't play nicely with existing Cygwin installations (see <http://cygwin.com/acronyms/#3PP>). The approved way of installing Cygwin is using the setup.exe tool.
I totally agree that one should use Cygwin setup.exe to install a Cygwin-based application. However, you can just wrap setup.exe and a local repository with a base package holding all the packages to install with some Windows install program to get single executable setup package.
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