Over at the Volokh Conspiracy, Sasha Volokh has been struggling with the question of the moral uniqueness of the Holocaust. Or, rather, he hasn't been struggling; he's "not into" it. Rather, his readers have been struggling to convince him otherwise. See here and here for followups. His basic point can be summed up here...
Alas, I still don't buy the moral uniqueness. To repeat my point from below: the Holocaust is evil because killing six million Jews is six million murders, and committing six million murders is highly, highly evil. Really evil. But not more evil than killing six million other innocents. (As I've mentioned below, the Holocaust also has lots of characteristics that make it especially grisly, especially memorable, especially important as a cautionary tale, especially relevant in a world of ethnic warfare, etc.; but you can be all those things without having extra evil.)
...but you should read all three links (don't worry; they're not too long) so that you understand the context.
Sasha has already rejected several explanations, so I'm not sure he's going to buy this one, either, but let me have a go at the topic: Sasha mostly rejects the idea that motive matters. But the Holocaust is morally unique precisely because there was no motive, because it was so senseless. There have been other mass killings in history -- though few on the scale of the Holocaust -- and some of those were also ethnically motivated. But, to my knowledge -- and I acknowledge here that my knowledge of history is incomplete -- the Holocaust is the only instance of genocide purely for the sake of genocide.
Some cases of mass murder -- the famines in the Soviet Union, China, North Korea, for instance -- were the result of attempts to implement and/or maintain economic "reforms." Insane attempts, to be sure, and the deaths were a foreseeable consequence, and the perpetrators didn't mind. But the primary idea wasn't to wipe out all these people; the idea was to make an omelet without caring how many eggs got broken along the way. (Clarification: to an extent, these famines were targetted at specific groups of people, people who presented a problem for the regimes. But that leads to my next point.)
What about the ethnically-based mass murders, where the killings were intentional? Well, most of those cases were actually the result of conflicts over land, resources, etc. Saddam Hussein wasn't gassing Kurds for fun; he was gassing Kurds because there was armed Kurdish opposition to his government and he was trying to suppress it. The Bosnia/Kosovo ethnic cleansings were similar. The westward expansion of the United States, which some have termed "genocide," was a straightforward conflict over land. Indians had it, Americans wanted it, and the only way to get it was to take it by force. I don't mean, of course, that these arguments excuse the killings of innocents, particularly on the huge scales in question. These cases were terrible, horrible, no good, very bad. But in none of those cases was murder its own justification. General Sheridan may have said -- or may not have -- that the only good Indian was a dead Indian, but he didn't act on it. That is, while he may have killed Indians -- while many people did -- nobody was going around New York City ferreting out all those with a hint of Indian blood and slaughtering them; nobody, to my knowledge, was even suggesting it. Saddam Hussein wasn't planning to invade Turkey so that he could wipe out their Kurds.
But the Holocaust? It's different. The Nazi goal wasn't to take territory from Jews. It wasn't to take resources from Jews. It wasn't to destroy armed opposition to the German government. There was no underlying reason for it; the goal was to wipe out Jews. Worse, it was such an important goal for the Nazis that even while fighting a continental war for their regime's survival, resources were diverted away from the war effort to continue the Holocaust.
Is that different than merely killing people you come across? I think it is. I think killing for the pure pleasure of killing can be distinguished -- and can be reasonably said to be morally worse -- than killing to accomplish an end, no matter how evil the latter is. Sasha talks about the Holocaust being "not more evil than killing six million other innocents." I'll stipulate for the sake of argument that if a group decides they're going to kill six million names at random from the phone book, that would be just as bad as killing six million people in order to wipe out a specific ethnic group. But that isn't what happened, and as far as I know, that has never happened. As such, the Holocaust is morally unique among actual historical events.