Raspberry Pi Stand-Alone Programmer
QCPete 
Robust Adapter Cable
I also decided to go with a custom adapter board. The ribbon cables on the MKIIs were always dying on us, so I wanted to ensure we wouldn't see any of those issues. I went with a 1x6 jumper cable and a custom little adapter board to mate with out standard 2x3 AVR programming header.
This worked out pretty good, but as scope creep settled in, I did revise this once. The V2 had the target VCC come back on the 6th pin, so that could be an option to use in setting the target logic level.
This added feature actually came with a second feature I didn't anticipate. If you jumper both the "target supplied" VCC and one of the Raspberry Pi supplied jumpers (3.3V or 5V), then you can power the target. This was super handy for those programming procedures of bare ICs. Now our techs only have to plug in a single cable for programming and power. Wahoo!