I was browsing through the mailing list and never saw the solution, but I'd like to note for the record for using Nutch with Windows, that the bin/nutch file needs to use *nix line breaks.
So if you get an unexpected \r error on run in Cygwin, that's because Windows users have \r line breaks, and *nix users have \n So in VIM if you do a :set ff=unix :w it runs fine.
