Hi,
Very nice instructable, I am so looking forward to play with my old NES controller again; i need to play "Super Meat Boy" with the old feel!! 
However i can't seem to get mine to work. I think i followed all the steps correctly upto the 'test it now'-fase.
I uploaded the software you supply on the instructables website on my rbbb with arduino0016 (after deleting that preferences.txt file), but i have the idea the supplied lib maybe isnt in order.
After pluggin in the USB my pc doesnt recognize the board as an usb HID device (I tested on linux and windoes7).
I noticed in usbconfig.h that the VID & PID werent the 'free' HID pair...
I changed it to this:
#define USB_CFG_VENDOR_ID 0xc0, 0x16
#define USB_CFG_DEVICE_ID 0xdf, 0x05
After changing this, still no recognition ;(
The only thing i have different on my setup is that I use 1,3W zener diodes (3,6V), instead of the 500mW you list. This surely cannot be the problem??
I first tested this without the 10 cables from the NES-pcb. I assumed the atmega328 with your code on it should surface as an usb HID with just the neccesary element to get the usb-cables sorted. Is this correct?
I also tested it with the 10 cables attached: no difference.
The files i use: http://opmerk.nl/klz_Nespad.tar
Could you please please please help me out / point me in a direction i can try? So far i havent been able to understand the v-usb-lib
update
So i got the 500mW zener in, built the breadboard setup with them.
+
- Attached the +5v of the USB cable to a 5V pin on the RBBB, and attached the Ground of the USB cable, to the Ground of the RBBB
- I put an 104 capacitor between +5v and Ground
- made the right-side connections of the picture
upload the software from the instructables website
unfortunately i get device not recognized errors when i plug it in.