Well here's the pinout, done just now by myself.
It uses a 32 pin (MLF) Cypress CY8C2134-24LFX PSoC. This pinout can be found online if you want to desolder the IC and use it for your own use.
http://pdf1.alldatasheet.com/datasheet-pdf/view/124940/CYPRESS/CY8C21434-24LFX.htmlThe iPod connector pinout is as follows: (This is an iPod Video CW, so I'm not sure if other iPod CWs are any different)
Clickwheel facing you, Pin1 at the top: (like how it is in an iPod); [iPod pin; IC pin; pin description]
1 Pin 17; XRES (Active high external reset with internal pull down. This is covering pretty much the whole FPC)
2 Pin 2; P2[7], IO, Analog Mux
3 Pin 3; P2[5], IO, Analog Mux
4 Pin 4; P2[3], IO, Analog Mux
5 Pin 5; P2[1], IO, Analog Mux
6 Pin 6; Power, Switch Mode Pump (SMP) connection to required external components
7 Pin 7; Vss, Ground connection
8 Pin 8; I2C Serial Clock (SCL)
9 Pin 9; I2C Serial Data (SDA)
10 Pin 10; P1[3], IO, Analog Mux
11 Pin 11; I2C Serial Clock (SCL), ISSP SCLK
12 Pin 28; Vdd, Supply Voltage
Hopefully this helps someone, as I couldn't find a pinout of ANY clickwheel online, and I'm sure others have wanted to know the pinout as well.
It communicates over an I2C bus which most MCUs can communicate with, making it an easy target for projects.
Cheers.