How do I start a second instance of a program from Unity's launcher?
You now can start a new instance via a middle clicking on the launcher icon.
Click the launcher with the middle mousebutton.
At the moment, the only possibility to start a second instance, is using the Applications view, in the sidebar or the Ubuntulogo at the top.
If you want a second Instance of the terminal you must select "New Terminal" in the File Menu from gnome-terminal. It's similar with Nautilus. But (currently) it's not possible to start more than one instance from the Launcher