In presuppositional apologetics, we show that the presuppositions, or the fundamental beliefs, of all who reject Christian theism are riddled with self-contradictions. Their metaphysical assumptions ("view of what exists and is real") provide no coherent foundation for their epistemology ("how they know") and ethics ("how they should live their lives"); and, considered jointly, their metaphysics, epistemology and ethics are mutually incoherent. This is a fact that most unbelievers do not confront, as they refuse to engage in self-reflection and critical examination of their beliefs. Even when confronted with these contradictions, unbelievers, unless convicted of their sin by the Spirit of God, will continue to irrationally hold to their self-styled "rational" unbelief, rather than turning to the only rational position, Christian theism.
For instance, unbelievers -- on the basis of the presupposed properties of a godless universe -- cannot give coherent accounts of their "knowledge," in general, or of their moral judgments.
In particular, when it comes to morals, the unbeliever has no basis whatsoever for making moral pronouncements. This follows directly from the typical belief of the so-called "scientific" worldview that only science yields knowledge. This viewpoint is called scientism. In that epistemology (based on the so-called "logical-empirical approach"), only things that are empirical or can be logically deduced are known1. Ipso facto, that belief excludes moral knowledge.
First, moral laws are not perceived via the senses (empirically). One cannot see, touch, taste, hear or smell moral laws. Moral laws (like laws of logic) are immaterial, they are not natural. They are not discovered "in a test tube." Second, moral laws are not logical tautologies. Thus, by the atheist's espoused (and non-self attesting) epistemology, moral laws are inaccessible to human knowledge. Moral laws are unknowable and unknown. This reduces the atheist to absolute moral skepticism.
The result is that for the unbeliever, moral pronouncements are arbitrary and matters of subjective opinion. Moral laws are, then, just social constructions, whether by custom or legislation. In the case of legislation, they are established by power -- either a consensus of a majority in democracies (political power then determines the morality of the age) or by brute force in totalitarian regimes and dictatorships. There are American secular norms; there are Islamic fascist norms, communist norms, Nazi norms -- all of which, inter alia, are arbitrary.
So far, we are discussing the self-contradiction of those who believe in "morality;" albeit an unknowable, subjective, non-absolute code of conduct. Of course, this means there really is no morality in any sense; there is only legality as encoded in arbitrary legislation and conformity (or non-conformity) to changing social customs dictated by individual tastes. Today's "evil" may be tomorrow's "righteousness." This further means the unbeliever has no basis for making a "legal/moral" dichotomy or the claim that there are "unjust laws" ("That may be legal but it is morally suspect").
In addition, we should mention that those who espouse the epistemology of scientism typically hold to some form of materialism. In that case, not only are moral judgments unknown, but morals would not exist. Morality does not exist (or inhere) within the laws of physics. So metaphysically, there is no foundation for morals in a materialist universe. It has oft been correctly stated that one cannot argue from "what is the case" (mere descriptions of the natural state, which is all science ever does) to "what ought to be." There is no "ought" in the laws of physics. All that "is" follows solely from physical processes obeying inviolable physical laws. In the atheist universe, everything "does what comes naturally." No "wrong" ever occurs; "right" and "wrong" are not properties of matter.  Everything is merely matter in motion. [We should add that no mental freedom, volition, or rationality would occur either, as all "thoughts" and vocalization of such would also be the inviolable results of "what comes naturally."] The moral theory of the atheist is bankrupt, both metaphysically and epistemologically.
In conclusion, all of the above destroy the pretense of atheists and agnostics who claim to make "moral" pronouncements. When you hear a proponent of scientism make pronouncements on moral judgments, just remind him (that on his own terms): "You don't know what you are are talking about."
1 Of course, this presupposition of scientism is neither an empirical observation nor a logical tautology. It is, therefore, not a scientific statement and, thus, not an object of knowledge. It is self-refuting. ↩