I believe that any metric of consequence which takes into account only suffering when making the choice of "torture" vs. "dust specks" misses the point.

No, that was the point alright. If you don't believe me, ask Eliezer.

If that's Eliezer's position then Eliezer is wrong. I have no choice but to treat him as such until such time as I am introduced to a persuasive argument for why some consequences are "fit" for consideration whereas others are "unfit". I cannot, of my own accord, derive an intelligible system for doing so.

moral responsibility

If it's not happiness, I don't find it intrinsically important.

1) I do not view "happiness" as intrinsically important, but I'm willing to stipulate that it is for this dialogue.

2) I made no argument of 'intrinsic value'/'significance' to moral responsibility. I said instead that how the choice would affect what we deem morally responsible would have consequences in terms of the utility of the resultant society.

A society that lives by utilitarian principles would be better than any possible society that doesn't. As such, wouldn't encouraging society to live by utilitarian principles be a good thing?

Yes, it would. But real utilty trumps pseudo utility.

If you don't choose torture over an unimaginably worse alternative, you're encouraging people to choose the unimaginably worse option.

Certainly. Assuming that's what was done. The entire point of my argument was that the net impact of a given choice on utility should be what is considered. Even if we allow for the 3^^^3-dustspeck scenario to be "unimaginably worse" than the single torture, the primary and secondary consequences of the 3^^^3-dustspeck scenario are by no means clearly "unimaginably worse" than the primary and secondary consequences of the torture scenario.

Out of curiosity, what about the "criminal" scenario? I understand that what they do to criminals isn't technically torture, because the suffering from imprisonment is slower or something to that effect, but that isn't morally relevant.

Strike "technically". It isn't torture. Imprisonment (with the exception of extreme forms of solitary confinement) in no way compares to the systematic use of pain and extreme conditions to disrupt the underlying psychological wellbeing of another person. Furthermore, the torture-vs-dustspeck question is of a ceteris-paribus ("all other things being equal") nature. Regardless of which choice you wished to consider, if it was phrased in terms of the suffering being inflicted with cause, then the two are indistinguishable -- though I personally am unable to imagine any person being capable of deserving being "terrifically tortured" for fifty years (or a month, or a week, for that matter. I could see a day for a child rapist. But that's neither here nor there.)