Implementing HID input device with an Atmel AVR32
Download Atmel Studio 6 and check out the examples (integrated into the Studio). If I remember correctly there even is an example for HID Devices.
Of course there is a fully implemented USB stack available upon which you can still build upon.
Furthermore, there are examples for various other USB devices (Mass storage, ...)

You might also want to refer to the following application notes:
http://www.atmel.com/Images/doc8446.pdf - USB Device (HID Keyboard)
http://www.atmel.com/Images/doc8499.pdf - USB Device (Generic)