The current system of launching applications is challenging in more than this one way. It has a completely arbitrary grouping ("applications" and then "more applications"?), it doesn't provide sub-folders and freedesktop.org compliant categories... It's a mess as soon as you have more than only a few apps installed.
This solution proposes that the community comes up with an alternative application launcher that can be installed from extras and can be placed on the desktop as a shortcut. (Maybe the Maemo UI even provides better places for such things? Like the app launcher being an entry in the menu that comes up when you press the power button? Or the app launcher comes up when you press the camera key?)
This application launcher could be highly configurable. It could allow the user to make it appear as a desktop shortcut or elsewhere. It can allow to re-arrange icons, create folders, etc.
It should also intepret the categories of the freedesktop.org standard, so that application develpers can hint where to put a menu entry in the .desktop file.
I propose this solution because such a 3rd party application launcher would solve a few issues at once and make users independent of Nokias UI design decisions in this area.