I am running a virtualized Windows 8 installation on VMware Worlstation in Ubuntu 12.10 and this can be confusing since the window manager uses the same key as my Windows machine to open the launcher. Therefore I use to disable the super key in Ubuntu so that only my Windows machine responds to the key.
This is one way to disable the super key from a console window as the user you are logged in with:
# dconf write /org/compiz/profiles/unity/plugins/unityshell/show-launcher '""'
This command does not require a logoff or restart so you can test the behaviour of the Windows super key immediately.
You might have to install the apt-get install compizconfig-settings-manager package if this command does not work.