Well, I don’t like when my PC goes beep-beep at 2 a.m. and everybody is sleeping!
So I’ve found a radical way to disable it: simply forbidding Linux to load the PC speaker kernel module.

Edit /etc/rc.local and add:

rmmod pcspkr

That’s it.
If you want to disable it right now simply type the same line in a terminal, as root (or use sudo):

# rmmod pcspkr