we have a project that uses EMX board which seems to be fading away, which of GHI boards is the best candidate to replace it electronically, in terms of layout and pins i guess
What makes you think EMX is fading away?
But the best replacement for EMX would be the G120.
Similar features, lower price, a bit more power.
The only downside compared to EMX is that it does not support building Ethernet (with PHY). You need to use ENC28 for wired networking (if you need it). We have successfully used a ENC28 clone on our custom G120 board.
Not sure how difficult it would be to modify the layout of a board to replace EMX with G120, since we just started with our board when G120 came out, even that our initial plan was to use EMX.
Why do you think emx is fading away? It is in full production and even with a lower price now.
But if you do not need Ethernet then g120 is even lower cost.
sorry for retiring the EMX too soon (i guess) but this is the impression i got from the forums and other websites for .NETMF, maybe i was wrong
as for the replacement board, money is not the mine concern but as little changes as possible for the electronic design and components aspect, G120 is the best fit?
As Gus sayed, if you don’t use Ethernet, the change should be in the routing only.
Ethernet would require a couple of additional components on the board.
What about application protection? 
If Im right it is missing on G120 firmware…
It’s missing since FW Version 4.2 (for all boards).
And since G120 is not supported by FW 4.1, yes there is no FW Protection for G120.