I’ve created a Google code project with the snappy title of avr-usb-rgb-led. It is based on the hid-custom-rq example from AVR usb examples. I’ve added 3 new commands, one for each LED. It uses a software PWM to control the brightness of each LED based on the value set.
There is a coresponding program using libusb which allows you to send the commands, it simply allows you to set the colour of the cube with an RGB tuple on the command line.
To get the code you need to check out using subversion. To flash the chip you probably want to use the makefile.