How do you mute from the command line?

Assuming you're using ALSA driver, run:

amixer set Master mute   
amixer set Master unmute

Or, you can just use:

amixer set Master toggle

to toggle mute on and off.

This worked for me when others didn't:

amixer -q -D pulse sset Master toggle

This is from the link in nutty about natty's comment to the first answer:

In my setup sometimes amixer unmute fails for some reason. Therefore I'm using pactl in my scripts:

to mute:

pactl set-sink-mute 0 1

and unmute:

pactl set-sink-mute 0 0

Tested on Ubuntu 12.10.