I have recently heard and read the phrase 'moral equivalent' several times, and after thought, I have no notion what it means. See a few examples here. The natural meaning would seem to be that, given two cases, one can, for all moral purposes, substitute them for each other (in what way?) without change (of what?). But this can't be what is meant, because the phrase is often used of things that are clearly not intersubstitutable. If it just means the two cases are in some way analogous, it can't be reasonably used for the sorts of arguments in which it is employed without clarifying in what way and to what degree they are analogous. (I have similar problems with 'moral standing' when used comparatively.)
(Incidentally, even setting that aside, I find none of the arguments in the Reason article linked above even particularly interesting, since they are as sloppy as all get out. The term 'holocaust' is misused; most of the rhetorical questions could be consistently answered by a right-to-lifer with a "That doesn't necessarily follow"; the 'thought experiment' is ludicrously stupid, since it doesn't support what it is supposed to be supporting; and the last paragraph requires the erroneous assumption that the only reasons for which one could want to halt stem cell research are theological. It would be helpful if people actually used rational arguments on this sort of topic, particularly in a magazine called "Reason". But Eric Muller has a good review of Malkin's internment book, which quite redeems the December issue. And, to be fair to Bailey, he does have a good article or two about.)