I sometimes feel a little bit weird, when I see criticism of the theology of a religion (or some other philosophy I don't hold), I almost always think of several ways for the theology/philosophy to reasonably parry that jab. The lighthearted stuff in MrDeity, the serious back-and-forth in the debates I occasionally read, etc. It's not just the positions I disagree with, it just seems that once you get past the initial bumpy ground at the root of most philosophies or faiths, it's hard to land decisive blows on a faith (provided you're just looking for internal consistency and preservation of theme/character of relevant figures, if any).
In the most recent Mr Deity (as of this writing), there's the question as to why an all-knowing deity would bother sending people to Terra if it knew beforehand which people would merit heaven and which would not; fun jab, but the simple idea of earning it, even in the kind-of strange concept of a determinism rooted in theology, is sufficient justification. And as an example of the deep problems that come from some theologies, when I was in college, taking a class on eastern religions, we were studying sects of Hinduism and I posed the question, if there is an ever-expanding number of people on Terra, where do the new souls come from? Later in that class I thought of a highly unorthodox solution to the problem: a single soul looping through time and every single being in the cosmos including all the afterlives in that sect of Hinduism. There is, I am sure, a less weird solution.
It feels like our logics are generally too weak to decisively attack most of these philosophies (even as their claims to be "necessarily true" and all alternatives to be necessarily false can't be advanced, for the same reasons; we can't decisively kill their plaisibility).
And we rely on occam's razor, hunches, and a lot of heuristics that seem pretty solid to justify atheism. I do hold that it's the most sensible position, and I am pretty sure it's right, but there are too many ways to build philosophies to decisively and entirely win. At best we can win by showing how great that grab bag of arguments is; predictiveness, philosophical simplicity, empiricism, human fingerprints on all those faiths, and of course the ignorance of the sciences present in ancient texts. Plus we can study how people come to faiths and undermine that. I think if we ever really want to go the philosophical route though, we have to go right at the heart of the core logic (and the core of the general emotional appeal) of each system. At that level the philosophies/religions have very little wiggle room. Souls, sin, central figures, natures of gods, afterlives. A solidly non-traditional view on any of these (or a completely secular one) collapses most faiths. Maybe.
It still feels like we're assaulting castles with pocketknives though. And not just us atheists; serious and rigourous debate between the different faiths tends to look the same; the Monitor and the Merrimac. Or to use a better metaphor, because philosophy is such a flexible realm, how do we catch a butterfly in a N-dimensional space where N is very large? There are too many different ways it might dodge. We might try to disallow it from dodging in some complicated paths using occam's razor, and use argument maps to track where it's been, but if it's allowed to adapt (rather than fly it's pre-run flight path), it still can elude us arbitrarily.