Hypothetical moral dilemmas are not a popular topic in some circles. I recall Darwin Catholic, in particular, decrying hypotheticals of the Trolley Problem sort as worse than useless, as somehow pernicious. In this I think he's quite perceptive, because I think that moral dilemmas and the way human beings react to them tend to undermine theories of the conscience as moral perception.
For example, the classic way to discomfit a deontologist is to ask her* to imagine she is hiding a family of Jews from the Nazis, and that an SS guard asks her point-blank whether she is hiding anyone.
Of course, her predecessors have devised scores of ways to handle these scenarios. She might bite the bullet and say she's bound to tell the truth even then; she might say that the duty of truthfulness carries the implicit condition that the hearer is 'entitled' to the truth; she might justify mental reservation or other equivocations. But if she is anything like me, she'll admit that each of these options still leaves her with a sense of moral conflict; she still feels she ought to do all in her power to save that family, and this really seems to include lying as convincingly as possible, without hesitation or scruple.
I'm not aiming (here, at least) to belittle deontology, only to note that sense of moral conflict that persists even when she's confident she has the "right answer". There are hypotheticals that similarly perturb utilitarians, or virtue ethicists, or the adherents of any particular system of morals; and only by dint of self-delusion can we pretend to be perfectly reconciled to all of these tragic scenarios.
What does that signify? To me, this effect is poorly explained by the notion of our conscience as a form of moral perception, and better explained by the hypothesis that our conscience is simply a collection of evolved drives of a sort we call "moral", extended and harmonized by culture, habit, and our own thoughts.
We have a drive to be truthful (more to the point, there is a drive observed in primates as well to punish the trickster or cheater, and we have internalized it), and we have a drive to save the lives of that family (of course, the development of more universal forms of altruism deserves a discussion in its own right), and in the hypothetical above, these drives conflict with one another. That's why our deontologist can't be at ease with any solution, no matter how cleverly she seeks "the right answer". Of course, it doesn't bother a consequentialist in any significant sense, because he* hasn't habituated himself to consider lying per se as the reprehensible sort of trickery or cheating unless it hurts someone. As I said, we can train and modify these instincts over time.
The only problem is that we'd really like to treat this conscience of ours as if it more resembles our physical senses than it does our other emotions. It seems that to do otherwise would be to rob it of its prescriptive authority, to reduce the conscience to a matter of feeling and taste. But it can be no other way; if the conscience is a perception of an external right and wrong, how can it reproach us even as we follow it?
"Well, well," you say, "granted all this, you haven't done a thing to dissuade me that there are objective moral values; it's perhaps more difficult to discern them than I'd otherwise assume, but clear reasoning about life should do the trick!"
To that I say, "Bravo! I have much more to say, of course, on our human reason and indeed on the whole of moral reasoning; but you're quite right about the limited scope of this inquiry. I seek to debunk, not morality, but the conscience as its sure guide, and to lightly suggest that we can better form that conscience in accord with what we think is true."
But of course, you did not even grant me that much, because I haven't made a very good case at all, and because very few of you would be inclined to agree with me in the absence of a stellar argument. I eagerly await your disagreements, so that I can figure things out a bit better in the comments...
*A note on my perceived failures in gender-neutral language: I've decided, instead, to use a quantum superposition of "he" and "she" for an indeterminate hypothetical person. By reading this blog, you are collapsing the wavefunction.