I had a Cygwin installation on Windows x64. Recently, I found that its setup program could not pull the package list, claiming that the mirrors could not be found. It turns out that now Cygwin has split off into x86 (for 32-bit Windows) and x86_64 (for 64-bit Windows).
I tried the x86_64 and found it lacking many packages that are present in the x86 branch. In addition, there were many other problems too. So, if you are using a production system based on 64-bit Windows, you might still want to use the x86 Cygwin. Both of them work on 64-bit Windows, but the x86 version is bound to have fewer problems in the near future, until x86_64 version gains stability.