The USB Armory comes with a nice little LED on board. In the default Debian image, it is set up to blink based on CPU usage. To control it manually, take the following steps:

Unload the ledtrig_heartbeat kernel module:

#> modprobe -r ledtrig_heartbeat

Turn it off:

#> echo 1 > /sys/class/leds/LED/brightness

Turn it on:

#> echo 0 > /sys/class/leds/LED/brightness

If you want to set it to half brightness (this is apparently a bit of a hack):

#> modprobe -r leds_gpio
#> echo 123 > /sys/class/gpio/export
#> echo in > /sys/class/gpio/gpio123/direction

Once you’ve unloaded leds_gpio, to control the LED:

#> echo out > /sys/class/gpio/gpio123/direction

to turn it to full brightness, and

#> echo 1 > /sys/class/gpio/gpio123/value

to turn it off, and finally

#> echo 0 > /sys/class/gpio/gpio123/value

to turn it on.

And last off, to blink it really quickly:

#> while [[ 1 ]]; do
    echo 0 > /sys/class/gpio/gpio123/value
    echo 1 > /sys/class/gpio/gpio123/value
    sleep 0.05
done

I take no responsibility if doing that damages your LED.