One of the problems with the Atmel ICE, like the JTAG-ICE before it, is that the headers on the actual debug probe are backwards, so the 50-mil cables are not just straight-through. This makes it much more difficult to find ready-made replacements.
I got around this by making a small PCB that plugs into the end of the ICE and provides standard 100-mil box headers for 6- and 10-pin ISP, JTAG/SWD, and 50-mil headers that are the right way round. You won't be able to use the Atmel cables anymore, but standard straight-through ribbons will work.
Details and links to the BOM/OSH Park project where you can order the board in this post:
https://www.eevblog.com/forum/microcontrollers/atmel-ice-50-off/msg1428410/#msg1428410A while ago I bought a pack of 50-mil ribbon cables for some dev platform (Netduino maybe?), but last I looked that wasn't available anymore. You can make your own 50-mil cables quite easily, though:
Connectors: Harwin M50-3300542
Cable: Digikey ME10G-10ND
I like the harwin connectors because they have a fully-enclosed slot for the cable to pass through that helps keep it aligned while mounting the connector.