This weekend while picking up some parts at RadioShack I stumbled upon a 3D Led Cube Shield for Arduino. The instructions are very detailed at first then as you go on you have to start problem solving. My favorite part is that the layout for the leds is drilled into the shield. You actually use the shield as a layout for the leds! How smart is that.
To get the sketch for Arduino to run the Led you have download the Support Files. The included sketch has a lot of examples and does a good job of describing each part. Although it will still be awhile until I'm able to write my own from scratch.