There was a great little tool that I think used to be in Ubuntu, but possibly another distro, where you could press a keyboard combo, and it would turn the cursor into a little crosshairs, and then if would kill the app running whatever window you clicked on. I don't remember what it was called, anyone know?
It was definitely xkill, I remember using it a lot during the early Ubuntu releases. I think the shortcut was ctrl-alt-esc, but its so long ago it was removed I no longer know for sure.