1. User Base: Cygwin is designed for Windows users who want Unix-like capabilities, while Kali Linux is specifically created for penetration testing and digital forensics professionals.

2. Purpose: Cygwin provides a Unix-like environment on Windows for easier command-line access and software development, whereas Kali Linux focuses on security testing tools and resources required for ethical hacking and penetration testing.

3. Pre-installed Tools: Kali Linux comes pre-installed with hundreds of security testing tools and applications, tailored for penetration testing, while Cygwin requires users to install additional tools and packages to enhance its capabilities.

4. Community Support: Kali Linux has a dedicated community of security professionals who contribute to the development and maintenance of the distribution, whereas Cygwin relies on a more general user base for support and updates.

5. File System: Cygwin uses a Windows-style filesystem and file paths, making it easier to integrate with Windows-based systems, while Kali Linux uses a Linux-style filesystem, providing a more familiar environment for Linux users.

6. Documentation: Kali Linux offers extensive documentation and tutorials on security testing methodologies and tools, geared towards professionals in the cybersecurity field, while Cygwin's documentation focuses more on usage and troubleshooting within a Windows environment.

In Summary, Cygwin is tailored for Windows users seeking Unix-like capabilities, while Kali Linux is specifically designed for security professionals with a focus on penetration testing and digital forensics.