Atmel is currently selling its programmer ATMEL ICE programmer as a bare PCB kit http://lt.farnell.com/atmel/atatmel-ice-pcba/debugger-atmel-arm-avr-pcba-kit/dp/2407171?ost=atmel+pcba . This is an enclosure I have designed for this PCB.
In few last pictures you can also see a very nice adapter from 50mil to 100mil headers which is designed by alank2
from http://www.eevblog.com/forum. It is featured in this post: http://www.eevblog.com/forum/microcontrollers/atmega328p-jtag-programmer-recommendation/msg578520/#msg578520
External dimensions of the enclosure 84mm x 48mm x 13.8mm (3.31in x 1.89in x 0.54in) .
I have used pieces of 1mm diameter fiber optic cable from old Toslink cable (optical audio cable used to connect HIFI equipment) to bring indicator LEDs ` lights on to the surface of the enclosure.
I have used screws of 2mm diameter and 8 mm length (with the head. Head diameter is 4mm and head height is 2mm)
For your printing convenience my Slic3r configuration screenshots are included in the zip file.