Just finished my 3rd play through of the original Shadow Hearts. The whole game has a strong occult backdrop with a variety of religious iconography peppered throughout the experience. Despite all this, I found the game to be very humanistic. Near the end, the heroes were really talking about the resolve and power of humankind, and the party of heroes actually goes up against "god" in the climax. The language alternates from referring to it as "God" and "a God", so it's not clear what the intended concept was. But it gave off a mildly noticeable "anti-theistic" vibe.
The Mass Effect trilogy, especially near the end, also seemed to take a strong naturalistic view of the universe, despite incorporating some "spiritual" characters. It's pretty clear near the end that whenever you choose not to affirm the personhood of your ship's A.I., you are making the "bad" choice. (Of course it doesn't help that the only options are "Agree with a philosophically untrue statement", "Say nothing" and "Disagree and be a big jerk about it".)