The BeagleBone Black includes four user controllable LEDs: USR0 through USR3. They can be controlled by going to:

/sys/class/leds/

In that directory are four directories, one for each LED. If you want to see what even triggers each LED look at the trigger file:

# cat /sys/class/leds/beaglebone\:green\:usr0/trigger
none nand-disk mmc0 mmc1 timer oneshot [heartbeat] backlight gpio cpu0 default-on transient

Note the brackers around heartbeat. The usr0 LED blinks a heartbeat to let you know the board is alive. You can disable this behavior and use it for something else:

echo none > /sys/class/leds/beaglebone\:green\:usr0/trigger

This sets the trigger to "none", and then you can turn on/off that LED with your own scripts:

echo 0 > /sys/class/leds/beaglebone\:green\:usr0/brightness # Off
echo 1 > /sys/class/leds/beaglebone\:green\:usr0/brightness # On

The BeagleBone Black has four user controllable LEDs that can be used in this fashion. More information can be found at elinux.org.