If this Cygwin build is stable then there are now 3 different ways to run sage under the windows OS (Virtualisation, Colinux and Cygwin).
From my point of view Virtualisation is the superior variant for general use. I see the following main advantages:
Speed: Calculations in Virtualisation reach almost the same speed as if run under pure Linux. Colinux and Cygwin (an educated guess) need noticable overhead, estimated 20 - 30 %. Maybe there could be some benchmarking of the Cygwin version?
Stability: With the virtualisation it is possible to use a stable OS as a base vor the VM, this means building and upgrading sage is easier and faster in a well tested environment. In contrary maintaining a stable cygwin variant can prove difficult and time consuming (past experiences of others which were reported here)
Generality: The Virtual image can run on any platform (not just windows) if there is the Virtualisation software available. VirtualBox is available with an open licence. I suppose there should be a version available for most systems out there. The Virtual version is just a plain version of sage, no special adaptions to the code base are necessary.
I think there is a very good virtual windows version available - including documentation and support. I'd rather see efforts united in developing this approach further than to split strength between different versions. But of course the Cygwin version could have some special applications or advantages that I am not aware of.