Solution 1:

Under Windows 7, here is the list of the keyboard shortcuts that manage multiple windows :

Win+d
Minimize all windows on all Monitors. Press again to restore previous state

Win+m
Minimize all windows on all Monitors.

Win+Shift+m
Restore previously minimized windows on current Monitor

Win+Home
Set all windows to Minimized on current Monitor except active

Win+Space
Preview Desktop / make windows transparent (May not work with all Settings)

Source : 127 useful Keyboard Shortcuts for Windows 7.

The OP notes that Actual Multiple Monitors has an option for "Minimize All command affects only the monitor with mouse".

image

Solution 2:

The other answer, although superior, is not as fun as mine. Take one active window and shake it. All other windows will be minimized. Then minimize that window

Solution 3:

I found another way to resolve this problem. I write autohotkey script to make all program minimize except some program. I often move Xshell and git command to another monitor, so I make them maximize again. The script like following, hope can help you.

#d::get()
get(){
    WinMinimizeAll
    WinGet, active_id, ID, ahk_exe Xshell.exe
    WinMaximize, ahk_id %active_id%

    WinGet, active_id, ID, ahk_exe mintty.exe
    WinMaximize, ahk_id %active_id%
}

You can replace "Xshell.exe" and "mintyy.exe" with another program and move them to another monitor then press Win+d to make all program minimize exclude you specified. How to run autohotkey you can click here.