I think it is important to draw a distinction between games that set up organizations or plots, religious in nature, that are meant to be taken on their own terms, like Silent Hill or Condemned, and those that earnestly intend to comment, negatively or otherwise, on faith, religion, or a particular belief system, like Dragon Age. It's a subtle difference, actually, but a very big one. Think about it this way: it's very common nowadays to cast Russia as America's big world-class enemy in games, but no one really bats an eye at it. But what if a game actually attempted to promote the idea that Russia really is a world-class evil that America needs to violently purge? The content of that game might not be noticeably different from a game like Modern Warfare or Bad Company, but the ideological difference would be very, very jarring to gamers- and, given how these things occasionally go, maybe to FOX News within a week or so.
It's true that the plots of Condemned and Silent Hill both center on the actions of the adherents of warped beliefs, but I don't think either one is meant to suggest anything unsavory about faith itself- either in its own context or in the real world. After all, in both of these games, the myths around which the two cults are centered are very real, and it is not the existence of the belief systems that is meant to be found repulsive, but the twisted beings and occurrences they are centered around.
Condemned never makes reference, even implicitly, to any real-world belief system. Silent Hill often uses symbolism and architecture meant to evoke Christianity, but the nature of its use seems to discredit the idea that it is making a negative commentary on real-world faith. One could easily argue that the juxtaposition of seemingly Christian symbology- or, in the case of Silent Hill on the PS1, an actual Christian church- warped by the Order's purpose is only used as a technique to create horror because it plays with the age-old idea of something benign and ubiquitous becoming malign and uncouth in a new context. Or to put it simply, the creepy Order churches in Silent Hill only seem as creepy as they do because the game assumes that real-world Christianity is more or less good.
On the other hand, there are games like Fallout or Dragon Age that are meant to explicitly invoke real-world religions, and they do so with varying intents and effects. In Fallout 3, the Church (or was it the Children?) of Atom is meant to lightly mock the concept of misplaced faith, but all in all it seems to be done rather tongue-in-cheek and I don't think there's any real malice there. Dragon Age does a pretty good job, actually. It's been a while since I played, but from what I remember, Ferelden was not a theocracy, but other than that the Andrastian church was definitely meant to invoke Roman Catholicism in the Middle Ages. Taking that as a basis, I'm actually rather pleased with how they handled it all. There is a question about whether or not the church's beliefs are misplaced, and that question is never definitively answered. There certainly was something special about Andraste, at any rate, but how that bears on the church dedicated to her deification never has any definite judgment passed on it by the game (nor, by extension, by its creators). The church and its adherents are shown to be flawed, but overall benevolent. The church is not perfect, but it does manage to do a great amount of good for the land. The people's faith, mistaken though it might be, strengthens Ferelden. That's a pretty grown-up way of framing it, and it helps add a lot of depth and believability to the setting- which is the strongest part of that or any BioWare game.
There are games out there that seem to view religion in a very negative light. 99% of the time, this means 'Christianity' as much as it means religion as a whole. One thing I've noticed is that, while not always the case, this is particularly common among Japanese games, and in Japanese media in general: manga, anime, what have you. The earliest example I can think of is the Ethos church in Xenogears, which is an obvious stand-in for Christianity. Naturally, the Church is not only false, but outright evil, perpetrating a world-wide conspiracy for its own benefit. Grandia 2 is a very similar example: the fictional Catholicism stand-in is not only false, but a scheme to revive pseudo-Satan and take over the world. I've never played Shin Megami Tensei, but from what I hear (even in this thread) it isn't exactly subtle about its notions of God. There are a lot of games like this, come to think of it, and I'm dimly aware of a lot of these plots occurring in anime, but I'm really not very familiar enough with it to say. Evangelion, of course, throws around a ton of faux-Christian symbolism, all of which is only barely deep enough to try and cast it in a negative light. Over-the-top evil or amoral caricatures of Christianity, usually Roman Catholicism, seems to be a pretty common thing in Japanese media, meaning there is a lot of spillover into videogames. I'd dismiss any of these examples, by themselves, as being flukes or attempts to be clever, but there certainly are a lot of them for them to be flukes- or clever. Whether or not it springs from any genuine disbelief or outright dislike of Christianity by the Japanese is beyond my capacity for speculation.
It's less common among Western developers, but it happens. Dead Space was mentioned, and it certainly deserves to be. I'd have put it in the first category if not for how overt the parallels to Scientology are. It's certainly deliberate, and whether their intent was to subtly bash Scientology or not, they certainly picked their target well enough- not enough people that play games care about Scientology, and thus won't be offended by it, but most will be familiar enough to understand the parallel.
Game developers need to be a little bit careful with this subject matter. As long as they make it clear that it's all just a game, they'll likely only draw the normal background level of fundie backlash, which is to be expected anyway. But on the rare occasions where a game developer might take a clear stance for or against a religion (other than Scientology, apparently) or religion in general, that's when things can certainly go haywire. We've yet to see what would happen if a big game actually did try to pull something like that; most games are considered to be pushing the envelope if they attempt themes or morals that wouldn't be out of place in Saturday morning cartoons. I don't really see it happening anytime soon, though; no one will care unless a big-money A-List developer tries something like that, and A-List developers aren't known for social activism- thank God.