In /etc/gdm3/greeter.gconf-defaults there's a line about the login sound. Turn it to 'false' instead of 'true' (and don't forget to remove the '#' sign from the beginning of the line, if there's one). At least the login beep will disappear.
Well it depends if the beep you are talking about is the one generated by the operating system or the motherboard. My pc beeps on a cold start but it's from the actual motherboard bios which you can usually turn off. You need to get into your bios utility screen and turn it off from there. Ian