Whatever I used it for, I would think - why am I doing this from this Windows box? I'll just telnet from UNIX and do it there (mainly file moving and intranet updates). The better solution was to ditch the Windows server and put in Linux Samba DCs. I always had the feeling that any task that Cygwin was useful for, was not "essential" and could be done another way without maintaining a giant Cygwin goiter.
Then I just thought - well, I'll keep it because it's nice to have grep. But it was more useful to have a Win32 grep that ran from cmd.exe. I could never identify a reason to keep it around because the type of things it was good for, could be handled with console programs for Win32. It was better to know how to make minor mods to a Windows server to get some of the same usefulness of the CLI tools in Linux.
Bottom line - if your Windows server has become essentially dependent on Cygwin to work, why not replace it with a real Linux box? It's sort of the same argument against dual booting.