I went into the start menu, clicked Programs/Cygwin-XFree86/editors/emacs. No response. (I had started the X11 server!)
So I looked at the properties of the emacs shortcut, and simulated the operation in a command window: cd c:\CYGWIN\bin c\:\CYGWIN\usr\X11R6\bin\run.exe emacs This failed to work. Typing just 'emacs' revealed the problem - the system could find the /bin DLL's but not the ones in /usr/X11R6/bin. Appending this directory to the path then made the start menu icons work: set path=%path%;c\:CYGWIN\usr\X11R6\bin A similar change to the system path enabled the start menu icons to work. But is it a recommended practice to include Cygwin directories in the standard system path? (It makes it easier to launch Cygwin applications from a Windows environment, but I'm worried about potential side effects). In my view it would be preferable for the path setting to be handled by the shortcut.