1. Cost: Alfred offers both a free version with limited functionalities and a paid version with advanced features, while PowerToys is completely free to use without any paid version.
2. Compatibility: Alfred is exclusively available for macOS, whereas PowerToys is designed only for Windows operating systems.
3. Features: Alfred primarily focuses on workflow automation, launching apps, web searching, while PowerToys is more inclined towards enhancing productivity with tools like FancyZones for window management and PowerRename for batch file renaming.
4. User Interface: Alfred comes with a sleek and minimalist interface, with a strong emphasis on search functionality, while PowerToys has a more customizable interface with a greater focus on power user tools.
5. Community Support: Alfred has an active user community that constantly develops workflows and themes, whereas PowerToys is supported and maintained by Microsoft but has limited third-party contributions.
6. Customization Options: PowerToys offers a wider range of customization options, allowing users to tweak various settings and features according to their preferences, compared to Alfred which has limited customization capabilities.

In Summary, Alfred and PowerToys differ in cost, compatibility, features, user interface, community support, and customization options.