One method that many religions use is to privilege a specific text, such as the Torah, (some version of) the Christian Bible, the Book of Mormon, the Koran, the Upanishads, the writings of the Buddha, or even Dianetics as having some privileged epistemic authority, i.e. promoting a specific text to scripture.
There are three problems with this tactic. First, why pick a scripture at all? Second, which scripture to pick? The first two problems are severe, requiring the adoption of arbitrary metaphysical principles which one adopts only to justify the choice of scripture and choosing some scripture in the first place. No logical contradiction or false-to-fact observation is entailed by adopting any competing scripture (or the principles necessary to choose one) or not adopting any text at all as scripture. Adopting a text as scripture is arbitrary, gratuitous and unnecessary.
Leaving these two severe problems aside, there's a third problem: All of the texts currently employed by the major religions (with the possible exception of Buddhism) contain passages absurd and ridiculous by any rational, scientific standard. Jeremy notes this atheist objection to Christianity:
Criticizing Christianity — or any other organized religion — is very easy, no doubt about it. There are far too many details, dramatic events, and literary flourishes to not strain even the most forgiving reader at some point.Jeremy's inept dismissal aside, the usual rebuttal to the charge of absurdity is the assertion that the scripture requires a multi-layered metaphorical interpretation, but this tactic raises a huge philosophical problem.
Determining the univocal literal meaning of a text is very difficult: Determining, for instance, what our laws and Constitution literally mean requires an enormous institutional edifice of lawyers, law schools and a hierarchy of courts. And this edifice pertains to documents that usually were written with great pains to be explicit, univocal, and literally comprehensible. One would expect even a very powerful—much less a supposedly omnipotent and omniscient—deity, a deity apparently capable of crafting the laws of physics with mathematical precision, to be at least as clear in its literal meaning as we ourselves are capable of in our law. It boggles the mind that one would even have to apply metaphor in the first place to the supposedly authoritative pronouncements of a deity.
Worse yet, it becomes entirely unclear what the theist means by "authority" at all once metaphor is admitted. Once we explicitly abandon the authority of the literal meaning, how are we supposed to decide what is metaphorical? How are we supposed to decide which metaphor or metaphors to consider? We can arbitrarily decide what is metaphor, or we can privilege some arbitrary principles to decide what is metaphor, but both of those tactics require exercising some authority higher than the text itself. Something cannot be both authoritative and subject to a higher authority. For instance, State and Federal law (in the United States) is not authoritative: Only the Constitution is legally authoritative; the validity of State and Federal Law (as well as ratified treaties) derives directly from the authority of the Constitution.
To interpret a text as both scripture and metaphor is logically contradictory: the text becomes both authoritative and not authoritative.
 "[U]nless the religion's assertions can be disproved empirically, the atheist's ridicule is nothing more than an appeal to 'common sense.'" The whole point is that the assertions are disproved empirically (i.e. scientifically): One cannot believe accounts of resurrections, virgins births, talking snakes and donkeys, a 6,000 year-old universe, and other purported miracles without rejecting empirical, scientific knowledge.
 And, perhaps, the pronouncements of the Supreme Court.