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Pros
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.
Cons
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.
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