I see here:
http://www.pgrs.net/2008/1/11/command-line-clipboard-access
that there's a way in linux and osx to copy to the clipboard from the command line. So I ran my cygwin setup.exe, but couldn't find the xsel package. I'm guessing maybe this package hasn't been ported to windows? Looks like there's a tool to do it in windows:
http://www.labnol.org/software/tutorials/copy-dos-command-line-output-clipboard-clip-exe/2506/
I guess I'll try that - but in the mean I figured I'd ask if anyone has found a good solution.