I haven't seen the inside of either project, but Wine seems like a much more difficult system. Cygwin is able to port large amounts of their stack from existing

I haven't seen the inside of either project, but Wine seems like a much more difficult system. Cygwin is able to port large amounts of their stack from existing software (mostly gnu), whereas Wine needs to reimplement almost the entire stack. Furthermore, Wine needs to maintain binary compatibility whereas Cygwin only attempts source code compatability.