Yes, the menus in Linux are a total chaos, and I realized that eversince I've been remastering Knoppix 3.6 trying to make it more human to my eyes. The problem is that the menu standards changed in time and instead of sticking to only one standard (the more recent...???!!!) they tried to shoot the bird and the rabbit with a single bullet. As you can see, they did succeed, but parts of the rabbit's liver are now in the bird's brains.
Seriously talking, I've been reordering the menus by sifting through and editing the ton of small .desktop and .directory files scattered through a lot of different places. Here's where you should dig to accomplish this: (I'm talking for Knoppix 4.0.2, but this may also fit for older and newer ones)

- /usr/share/applications and /usr/share/applications/kde, where mostly all the KDE packages keep their individual menu files

- /usr/share/applnk, where there is a menu structure with individual directories named for individual menu categories. In there there is a ".hidden" directory, which contains entries for the context menu "Open with" in Konqueror.

- /usr/share/desktop-directories - here are the start menu directories defined

- /etc/xdg/menus - here are also some start menu directories, defined as position and visibility

- /var/lib/menu-xdg - here are again the start menu directories, in the "desktop-directories" folder. Also there are 2 others folders, "applications" and "menus", which hold the individual entries for the whole menu and the menu structure respectively. They are not hard to understand if you study them a little

There is more of menus and the whole shebang but I just don't have enough patience to write it all now.

Anyway, my idea was to exterminate all the contents in these places except the contents of /var/lib/menu-xdg. So I moved all the .desktop files with the individual menu entries in /var/lib/menu-xdg/applications/menu-xdg after I modified them accordingly, I reduced to the maximum the files in /etc/xdg/menus, I deleted the .directory files in /usr/share/desktop-directories after embedding their contents in /var/lib/menu-xdg/menus/debian-menu.menu, I deleted everything in /usr/share/applnk except the ".hidden" directory after copying them to /var/lib/menu-xdg/applications/menu-xdg and so on...

The most painful process I've ever known...