These speakers were built out of a pair of USB powered desktop speakers that came with an eMachines computer, and the box my iPod Touch came in.
First, the components. I ripped apart the pair of speakers, and extracted the circuit board that ran the whole thing. Conveniently, all the inputs and outputs are labeled on the circuit board.
The iPod Box:
I drilled a whole in the side of the box for the volume switch to stick out of, and figured out the basic layout of the components.
The speakers just happen to be almost the exact height of the inside of the box. The speakers did not lie quite flush with the bottom of the box, so I modified the PCB so that they would. The box also had a cardboard liner around the edges, which I removed.
The next step was the batteries. The speakers were USB powered, meaning they ran of 5 volts DC, but I tested them with a few battery configurations and found that they ran perfectly well at the six volts produced by 4 AA batteries in a series. I cut the battery holders out of an old RC car, and soldered them together in a configuration that fit into a box.
I wanted to be able to dock my iPod directly to the box, but also be able to connect different types of mp3 players to the speakers. This posed a bit of a problem, as all players are laid out differently. I drilled a hole in the dock adapter that came with the iPod, so that a 1/8" audio cable could fit through. I kept enough cable so that if I would like to connect a different type of music player, I can just pull the extra cable out of the box. If I want to go back to my iPod, I just stuff the cable back in.
So sound can escape the box, I replaced part of the cardboard with fine steel screen.