Minimize all windows on the active monitor
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".
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