Command and Conquer is full of references.
In Command and Conquer Renegade, you find the tomb of Abel in the Temple of Nod.
The Brotherhood of Nod is a reference to the land of Nod Cain wanders through.
Cain = Kane, if you haven't figure it out.
General Shepherd gives you orders in C&C Tiberian Dawn.
General Solomon commands GDI in Tiberian Sun.
Kane dies multiple times but comes back every time. He's been killed twice now.
Kane can't be killed (reference to the mark of Cain).
There is a faction of the Brotherhood of Nod in Command and Conquer 3 called the "Marked of Kane."
Kane kills Seth, his right hand.
The Philadelphia, a giant space station containing GDI's headquarters, is blown up by a Nod nuclear missile. General Solomon commands from here, you could consider this an allusion to the destruction of the temple of Solomon.
In Half-Life 2, Father Grigori says random religious phrases while killing hoards of zombies. He also tells you to go to the church.
