If you are using Ubuntu and want to permanently disable the warning beep (I hate that thing when I have my headphones on), you can do so by editing your /etc/rc.local file. Open the file in your editor of choice and go all the way to the bottom of the file. At the bottom there should be a line which reads exit 0. Add a new line directly above this one and put this on that line: modprobe -r pcspkr. Save the file and this will turn off the system beep. If you want to turn the system beep back on, just edit this file again and remove the line that was added.