I don't see any option to run commands in Terminal in the run command dash (or is it lens?) of Unity. Is it available and deactivated, or is the feature missing altogether?
In any case, I think this issue needs to be addressed.
This isn't supported in Unity as it was in the GNOME Panel Alt+F2 dialog box, but nevertheless you can work around it by typing this in the Unity Alt+F2 dash:
gnome-terminal -e COMMAND
Where command
is the command you wish to run. Unfortunately due to a bug in Unity, you can't run a command with command-line arguments, using the Alt+F2 Unity dash. Hence, you can run:
gnome-terminal -e xeyes
But running:
gnome-terminal -e 'xeyes -display :0'
will fail.