Microsoft's Services for Unix / Subsystem for Unix-based Applications (SUA) might make an excellent replacement for Cygwin.
Since SFU/SUA interacts directly with the Windows kernel, it should be several times faster than Cygwin. This might make SFU an excellent platform for the porting of *nix applications to Windows.
With a good package manager, SFU can be the Windows equivalent of Fink (which is an excellent product). It should be able to compile MOST *nix applications with a few minor modifications.
Several package managers have SFU/SUA ports underway, including Gentoo and Debian. An easy way to install those should dramatically increase their use as.
SUA one other major advantage above Cygwin: It is included with Windows 2003 R2 and Windows Vista (Enterprise and Utimate)