Geogebra.desktop file is in /usr/share/applications but it doesn't appear in menu list. The desktop file: http://codepad.org/XeH6xdol
I've just checked the .desktop file, it seems perfectly OK. But it didn't appear in my menu either because I have the "use" flag on the Education category turned off. After I turned it on Geogebra appeared. Try setting the use flag to true in the menu_gen.lua file or in runtime from your rc.lua. I know that it is currently a bit nasty to dig in the widget files but I'm working on it.
Ok, it works :) Thanks!