Minime
If you are like me you probably have windows scattered all over your screen, and finding one of them using the taskbar is very daunting. Enter Minime, a small Windows utility that allows you to easily minimize any window to the system tray. Windows are minimized to a single tray icon, which minimizes the cluttering even more than each one having its own tray icon.

To minimize a window just switch to it and hit the hotkey Ctrl + Shift + z, which can be changed in the program's Options. To restore a window click on the tray icon and select it from the menu or hit the second hotkey (which can also be changed in the Options dialog box) to restore all the minimized windows.

I should also mention that it does not require installation. You just extract the executable from the downloaded Zip file, run it and it will create a file called settings.ini in the same folder if you change a hot key.

Visit Minime's homepage.