If you want to run a GUI application that doesn't have a menu entry (for example, gconf-editor), there's no need to fuss with a terminal window. Just hit (A! t +F2]. Then type the name of the program. If it needs to run with root privileges, just type gksu beforehand. If the program is command-line, check the Run In Terminal box. This will then open a terminal window and run the command but be aware that the terminal window will then close as soon as the command has finished, so you won't be able to inspect the output.
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