Well in Doom 3 when you shot some zombie, it would lay there stuck to the ground. But, in Half-Life 2 when you shoot someone on a hill or something, the body moves. Or if you shoot them and they fall into the water, the body floats. And Doom 3's A.I. isn't that great either, the zombies were either designed to act kinda dumb or the A.I. wasn't really that good.
EDIT>>> Don't get me wrong, I like both games and I've played both of them. But, I'll give Half-Life 2 the kudos because of it's realism. Because I like Halo 2 wayyy too much (Xbox LAN parties rock!), I'll give Doom 3 3rd (which is still pretty good when it comes to my standards).