I've made a script to workaround this issue. See at askubuntu: 
http://askubuntu.com/questions/36433/why-cant-i-use-the-unity-launcher-icon-to-minimize-applications-windows/39851#39851
   
See this working: http://www.youtube.com/watch?v=YfLxVsvUZTs .  


**Simplified Instructions**
  
**1)** We will need <a href="http://apt.ubuntu.com/p/xdotool";>XDoTool</a> and 
<a href="http://apt.ubuntu.com/p/compizconfig-settings-manager";>Compiz</a>.

   You can install these from the *Ubuntu Software Center* or by
clicking <a href="http://apt.ubuntu.com/p/xdotool";>here (xdotool)</a>
and <a href="http://apt.ubuntu.com/p/compizconfig-settings-manager";>here
(Compiz)</a>

**2)** Open Compiz (<kbd>Alt</kbd> + <kbd>F2</kbd> and type `ccsm` and hit 
<kbd>Enter</kbd>)  
    
**3)** Go to Commands and add `~/.minimize.sh` to one command (for example 
command 8):  
  
**4)** Then go to Button Binding and make a shortcut for it (for example 
alt+button1).
  
**5)** Now go to "General Options" and set a Button Binding to minimize (use 
the same modifier key of step "4" and Button2 - *if you want you can change the 
script as you like to fit another button*).   
 
**6)** Make a file named .minimize.sh at your home folder (`gedit 
~/.minimize.sh`). Paste this and save:  
  
<pre>
#!/bin/bash
#
# by desgua
#
# To minimize a window with Unity
#
# note: it wont work if multiple windows
# from the same app are open
######################################
sleep 0.1
xdotool click --clearmodifiers 1
win=$(xdotool getactivewindow)
eval $(xdotool getmouselocation --shell)
xdotool mousemove -window $win 0 2
xdotool click 2
xdotool mousemove $X $Y
exit 0
</pre>
  
  
**7)** Make it executable.   
    
**8)** Enjoy!  ;-)

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Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/733349

Title:
  Minimize windows upon clicking application's launcher

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