You can only control the active window with your mouse in a default Windows installation. If you need to do something in another window, you need to activate it first, before you can do so. This can for instance be done with a left-click on the window, the program's taskbar or system tray icon, or a keyboard shortcut like Alt-Tab to bring that window to the front.
Sometimes though you just need to work in that window for a second or so before you continue your work in the other window. This can be you blogging and listening to music at the same time, if you want to skip a song or change the volume for instance. It could also be useful in Windows Explorer when you want to drag and drop files to a folder that is not visible in the file manager's sidebar.
With Mouse Hunter installed and running in the background, you can control some window functions with your mouse even if that window is not active. This includes scrolling the window up or down or using other functionality that is assigned to the mouse wheel. For media players like SMplayer, this could mean going forward or backwards, or changing the volume of the media that is playing currently.
I often display two web browser windows side by side, for instance the admin interface of this blog when I'm writing an article, and the developer website of the program or service I'm writing about. Instead of having to click around to activate and re-activate windows, I can simply use Mouse Hunter to scroll on the developer site to read up on everything that they have to say about the app or service.
Another application is in Windows Explorer, where I may have selected some files that I want to move or copy to another folder in the sidebar. Once selected, I cannot scroll the sidebar without losing focus on the selected files.
Windows users who like to test the program's functionality can download it from the developer's website. The program is freeware and compatible with 32-bit and 64-bit editions of the windows operating system.