the menu items are populated from /usr/share/applications/hildon/*.desktop

You can remove item that can't be uninstalled from the app manager by removing it's desktop entry. Note that removing the desktop entry will not uninstall the application. If you decide to remove desktop entries, do so at your own risk. I'd suggest moving instead of removing in case you want have something back at some point...

I personally don't mind the few preinstalled things even though I don't use most of them.