I remember that there's a way to do it — place some prop_physics_override objects just above or below the ground, let the physics engine "settle" them to a more natural location, use a console command to update the source file with their current location, and then change them back to prop_static. I just forget what the console command is.
Also, I haven't tried this yet, but could you combine this method with the physics gun in Garry's Mod?
Also, I haven't tried this yet, but could you combine this method with the physics gun in Garry's Mod?