There are not many mods out there, but there are two worth trying.
First one SuperStorm. It improves skirmish mode, adds new AI behaviours, new units, maps and more.
http://www.insideearth.net/local_links.php?catid=17&linkid=32 (skip german, english is below) To install it just copy mod to WDFiles directory.
Second one is OperationX. It adds new Units, Weapons and Buildings. http://www.operationx.tk/ Installation guide on site.
Also there is SuperStorm for E2160:
http://www.insideearth.net/local_links.php?catid=10&linkid=94 which does pretty same thing.
http://www.insideearth.net/local_links.php?catid=10&linkid=100
IEO Rebalancing - if you want to play E2160 online. It balances races.