I would suggest KiCad:KiCad EDA
I already designed a custom board using KiCad for the edison, it works fine :-)
An alternative may be http://circuitmaker.com/
Here are some more:
The problem is that you will need at least 4 Layers and differentiell pair routing, what is missing in the most tools (it is included in KiCad and CircuitMaker)
KiCad is a good option. I also like EAGLE, if I'm not mistaken, there is a free (but limited) version of it.
I am going to try circuitmaker. DipTrace and KiCad.
Hope thay got a loot of components so I dont need to make all of them.
Need components from Atmel, Ti and Intel Edison
The free version of eagle is limited in
-max. 2 copper layers
-circuit board size 100x80mm (half euro)
-only one schematic sheet
KiCad has a small bib, it is working quite generic so you choose a symbol for the schematic and a footprint for the pcb design, not a whole component like in eagle
the basic packages are included
This thread could interest you :
I used Diptrace. In the thread, I shared the design files on my Dropbox.
I used the free version of Diptrace. This could be a good starting point for you. (Edison Footprint already made and tested)