After looking at James Wyatt's web site, I gave some thought to how I've treated religion in my RPGs. Religion is a terribly interesting phenomenon, so it appears repeatedly in my professional and personal work. While I'm an atheist, and while I see religious extremism as frequently a danger to liberty, tolerance, and justice, religion seems to have gotten fairly good treatment at my hands.
My first professionally published RPG was Ars Magica (designed with Mark ReinHagen). Ars Magica features a fantasy version of medieval Europe, with the medieval paradigm as fact. Thus, the Christian God is the ultimate power in Ars Magica. The PCs, wizards and their allies, are outside society and outside the Church. While the game generally portrays the Church as a rival power to the Order of Hermes, it is the wizards who are in the wrong and the Church that is in the right. It suits me that the wizards, with their great learning and power, don't also have the advantage of being doctrinally correct or in God's good graces. It would be insufficiently ironic for the Church to be wrong and the wizards to be right.
The wizards (literate, rationalistic, extra-ecclesiastic, non-feudal, and nearly scientific) clearly resemble modern people. The question of whether Ars Magica carries the sub-text that modern people are spiritually adrift is left as an exercise for the reader.
In my second RPG, Over the Edge, everything I could get my hands on got run through the irony mill, the weirdness transmogrifier, or both. The Edge's central house of worship, for example, hosts a weekly meeting of the "Mid-Eastern Compromise," Jewish, Christian, and Muslim believers meeting as friends and family. To me, this vision of moderate monotheists was an alternative to the traditional depiction of religious people (especially Christians and Muslims) as extremists.
In my personal campaign, some PCs met some true Christians (a al Philip K. Dick). These were a small band of faithful people waiting the imminent return of Christ. They knew that the last two thousand years of history were the Devil's illusion, a way to make Christ's life on earth seem distant and his imminent return unlikely. Not that it made any difference in the campaign, but these true Christians were right, which is why I haven't put the phrase "true Christians" in quotes.
In EVERWAY, various deities from around the world were all understood to be real. Greg Stolze suggested that YHWH (or at least his worship) appear in a published EVERWAY product, but I never went that route. YHWH as the tribal storm god from the top of the volcano would fit in EVERWAY, along with Zeus and Shango. Depicting YHWH thus, however, could have been taken as insulting by those who see Him as the One True God. As the One True God, He'd have a hard time fitting into the EVERWAY setting. Either He'd be a crazy solipsist, or all the other deities would be illusory.
In my D&D campaign, the PCs are from a holy culture that worships what amounts to a fantasy version of YHWH with their enemies as servants of what amounts to the Devil. (I know that the Biblical YHWH is not opposed by a Prince of Darkness. That's Mazda and Ahriman from Zoroastrianism. I'm consciously mixing ancient Hebrew and medieval European religious concepts because they're cool.) I made it clear to my players from the outset that irony and skepticism were not proper approaches to the setting. Just because the people of the PC's culture believe that they worship the One True God doesn't mean that they're narrow-minded, deluded bigots. In fact, they do worship the One True God. Sure, there's some irony in the setting. The Creator, for example, wouldn't pass muster as the modern depiction of God (a perfect source of unalleviated goodness), but then neither would Moses's YHWH.
My d20 Gamma World campaign was atheistic. Religion is essentialist, while I'm personally a non-essentialist. Fantasy worlds, no matter what their religious content, are usually essentialist. That makes religion a good fit for fantasy. Gamma World, however, is non-essentialist. It doesn't, for example, have alignment. In my d20 Gamma World campaign, there are religions (as in the real world) even though the gods do not exist (as in the real world).
Addendum: Religion in the real world, despite the protestations of the adherents of particular religions, is subjective and wishy-washy. Reality in RPGs is also wishy-washy, a reality by consensus. Maybe that's why I want religion in my RPGs not to be wishy-washy. I want religion to be what it claims to be in the real world: the truth. The whole world in an RPG is just what we (pretend to) believe. The subjectivity would be unpleasantly thick if the religion in an RPG were also just what the characters believed.