When comparing Cygwin vs Spartan, the Slant community recommends Cygwin for most people. In the question“What are the best power user tools for Windows?” Cygwin is ranked 18th while Spartan is ranked 45th.
Ranked in these QuestionsQuestion Ranking
Pro Additional packages available via Cygwin Ports project
Pro Better default terminal
Cygwin's default terminal "Mintty" is far better than CMD.
Pro You can run graphical applications
It has X Server.
Pro Can automatically save screen shots as JPEGs
Pro Clip Viewer
Just move the mouse over the clip slots and you see a preview in the viewer - Text or graphic.
Pro Log on System
Spartan will not only fill in your user name and password but will also select the three characters that some sites ask for from your memorable word.
Pro Script Langauge
Allows you to program multiple copy / paste operations from a single click.
Pro Encrypted log on system
Pro You can include the current date and time in clips
Have the current date and time added to your signature block in any format you wish.
Pro The window can be sized separately for multiple monitors
If you have two monitors, for example, one standard VGA, and the other a high-res 28-inch, Spartan is the only app that lets you choose a separate magnification for each.
Pro Auto shrinks digital photos when pasting
There is an option to have graphics reduced in size when pasted into emails or documents. Really useful if your pics are from a 15 Megapixel camera.
Con Many incompatibilities
A lot of tools don't actually work with Cygwin, and documentation is often sparse, so for many use cases, it's worth the small bit of extra effort to just run a full virtual machine.