Small-cube is a project mainly written in C, it's free.
4x4x4 LED Cube controller, using an ATMEGA8 series microcontroller
A display controller for a 4x4x4 LED cube. Based on a atmega8 microcontroller that is connected to 2 8-bit shift registers (74HC595).
The 2 8-bit shift registers can control one level in the cube at a time (4x4 = 16bits). The microcontroller scans through each level in the cube, turning each one on for 1/4 of the time. This happens so rapidly that to the human eye all levels seem to be on all the time.
The controller has an FTDI Serial -> USB converter. This enables programs on the host computer to control which segments of the cube lit up (i.e. for performing animations).