The Bible Online is a recent entry into the online real-time strategy (RTS) game market, but with the spin of playing biblical characters in the ancient near east. RTS games aren’t my cup of tea, but I might play for a bit just to see what they’ve done with it.
Rachel Wagner has an article on it over at Will God-Gaming Alter the Bible? | Culture | Religion Dispatches.
Related to that, James McGrath asked a while back if there were any ‘first-person shooter’ games based on the biblical material (Exploring Our Matrix: Israelites at War Video Game?). The closest I can think of are games like some on this list, or this one very loosely based on the apocryphal Book of Enoch – El Shaddai: Ascension of the Metatron.