This guide will show you the different patterns of the LEDs on the PS3 Controller, and what each one means.

Happens on: PlayStation 3, MotioninJoy
What it means: Controller plugged in through USB and is not recognized (on MiJ) or controller is not paired with system / given a controller number (on PS3).
Remedy: PS3: Press the PS button. MiJ: Plug in the controller to the USB port used during MiJ driver installation or reinstall the MiJ drivers.

Happens on: PlayStation 3, MotioninJoy
What it means: Controller is attempting to make a Bluetooth connection to its paired master (aka PS3 or your computer's BT adapter). If the LEDs are blinking like this for a while, it cannot find its paired master.
Remedy: PS3: Make sure the controller is paired with PS3 and the system is on. MiJ: Make sure the controller is paired with the BT adapter and make sure your BT setup is working.

Happens on: PlayStation 3, MotioninJoy
What it means: Controller connected, either via USB or BT, the LED lit indicates what player's controller it is (on PS3, MiJ v1-v3, v6+ with battery info disabled) or battery status, 4 being full, 1 being battery about dead (on MiJ v4-v5, v6+ with battery info enabled). This is normal operation.
With MiJ v6+ the LEDs can either be player controller number or battery status, the default for the v6 version of MiJ is to show battery status. To change which status you want the LEDs to indicate, choose the option you want in the DS3 tool, then press the Enable button.

Happens on: MotioninJoy v4-v5, v6+ with battery info enabled
What it means: Controller connected through USB and battery is fully charged. This is normal operation.

Happens on: PlayStation 3
What it means: Controller connected through USB, and battery is charging. This is normal operation.

Happens on: PlayStation 3
What it means: Controller connected through Bluetooth, and battery is dying. This is normal operation.
Remedy: Connect controller to PS3 through USB to charge it or risk the battery dying completely and a few frags
.

Happens on: PlayStation 3
What it means: A controller for players 5 through 7, add the numbers of the LEDs lit together to find out which player's controller it is. (eg 4+1 would be player 5's controller). This is normal operation.
1 - - -
1 2 - -
1 2 3 -
1 2 3 4
(repeat)
Happens on: MotioninJoy v4-v5, v6+ with battery info enabled
What it means: Controller plugged in through USB and is charging. This is normal operation.