I haven't played it very much recently, but the only online game I play that doesn't have an eGO division would be America's Army.
Version 3.0 will be coming out soonish, and is essentially an entirely new game running on Unreal Engine 3. I will probably be playing that a lot more when it is released, depending on how addicted I become to Left 4 Dead, and if my TF2 addiction wears off.