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The system that allows users to run X-Window applications on macOS is XQuartz. XQuartz is an open-source version of the X.Org X Window System that runs on macOS, providing a graphical environment for X11 applications.

By using XQuartz, macOS users can launch and utilize applications that were originally designed for the X Window System, which is predominantly used in Unix and Linux environments. This capability is particularly useful for developers or users who need to access applications or tools that depend on the X11 windowing system.

In contrast, Mac Ports and Homebrew are package management systems that allow users to install and manage software on macOS, but they do not provide an X11 server or environment. Therefore, while they can facilitate the installation of X-Window applications, they do not directly enable their execution through the X Window System. VirtualBox is a virtualization software that allows users to run other operating systems on macOS, but it does not specifically support running X-Window applications on macOS natively.