It was quite annoying every time I hit ctrl-alt-del in Gnome, the Logout window appeared – instead giving the combination to the active window (virtual machines, VNC, Remote Desktop connections, etc.).
Gladly this is just another global shortcut like any other ones (alt-F1 for menu, for example), therefore it can be disabled the same way: System menu » Preferences » Keyboard Shortcuts, in the window you can find under Desktop » Log out. Click on it, and disable it with a backspace.
Successfully got rid of an annoyance – “great success!” as my colleague said 🙂