Is iPod docking station just a USB with a different connector? Let's say I'm building a device with an iPod docking connector. Can I use standard software for USB on the device side? Are there any special considerations?

The device is supposed to play audio. Charging is good to have but optional.
Engadget has a great tutorial on how to create a custom iPod docking station, along with system configurations, etc. 

Hope this helps: 

How-To: iPod docking station/configuration