All of a sudden, one fine morning I found that the Applications Menu in GNOME on my Ubuntu 8.04 laptop was empty. When I clicked on the Applications Menu, all I got was a small rectangular box, about a few pixels in dimensions. I found a solution to this, (the solution was the first result that Google threw at me). This problem seems to occur when there is not much hard disk space left. When this occurs, you are unable to run alacarte even from command prompt.
The solution is to delete the applications.menu file from ~/.config/menus/ directory.$rm ~/.config/menus/applications.menuAfter this the Applications Menu is restored.