Update 1/9/2014: TL;DR version: Go to bottom of this post for a way to get Cygwin to be able to call non-Cygwin programs.
After having spent the ti
The best alternative I found is Gow (Gnu On Windows).
It's a lightweight alternative to Cygwin, about 10 times lighter. As far as I know the 130 tools installed with Gow are regular Win32 applications.