Interesting app... you can use its GUI, or use it via the command prompt [& scripts], and it remembers when you used it to hide an app, so you can close SilentRun Pro itself [the hidden app stays running], then reopen it to restore that hidden app's window. The fact that it can mute audio suggests that it's intended to hide games &/or video you don't want someone else to see without closing the game or app & signing out. It could be used to reduce clutter when you have multiple apps running, especially if you want the hidden app to continue processing whatever. You could probably also set up a script to start & then hide an app to monitor/log whatever every time someone logged into Windows -- those kinds of logging apps may show an icon on the Taskbar showing that it's running, which you may not want.
Installing SilentRun Pro just adds an uninstall key to the registry -- you can use the portable version if you want to avoid that -- while both the portable and regular versions use several .ini files to keep track off settings: Users\ [UserName]\ AppData\ Roaming\ silentrunoptions.ini, srexp.ini, srlan.ini, srsound.dll.
The comments posted on the download page seem to reflect a bit of confusion on why an app like SilentRun exists. One [*maybe* more socially acceptable] example might be to monitor online activity of a tween or teen without them being aware of it.