Comment 1 for bug 1349640

Just a few notes for what you are experiencing...

1. Items that you would not have write access to would be those installed system-wide. They can be "removed" from the menu by turning "Hide from menus" on. This writes a locally installed version to your home directory (~/.local/share/applications) that is hidden, this removing it from your menu. This is basically what alacarte does when you "delete" a system launcher.

2. If you are using Xubuntu (and possibly other distros), you don't see the items in the Settings category because they are added to the Settings Manager.