When comparing AutoHotkey vs Cygwin, the Slant community recommends AutoHotkey for most people. In the question“What are the best power user tools for Windows?” AutoHotkey is ranked 6th while Cygwin is ranked 20th.
Ranked in these QuestionsQuestion Ranking
Pro Can map keys to scripts
Pro Fully programmable
With a full programming language powering the hotkeys, including GUIs, it is powerful and flexible
Pro Scripting of common procedures
AHK allows full scripts to be created and used. it is very flexible.
Pro Allows for extremely easy remapping keys and buttons on your keyboard, joystick, and mouse
You can reprogram any key combination, including the Windows key with a syntax like this one:
that automatically remaps the H key to show a message box.
Can interact with any Windows program / dialog / form, filling fields, submitting data, etc., without dependency on the window placement.
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.
Con Programming language is primitive
The base syntax, inherited from the first version of AutoIt, is primitive (a bit like an improved batch syntax). But once used to it, it remains flexible and powerful.
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.