An incomplete list of atrocities that are arguably comparable to the Holocaust includes the fate of Native Americans in the US, Belgium's actions in the Congo, the Germans in Southwest Africa (present day Namibia), the extermination of the Roma during WWII, and the Rwandan genocide.  Those which aren't include what happened to the Poles during WWII, to the Ukrainians in the thirties, the Chinese at the hands of the Japanese or Mao, the Palestinians under the Israelis, the Bosnian Muslims under the Serbs, the Algerians during the Algerian War.

For American readers an analogy might be helpful. Occasionally one hears people complaining that one speaks too much about the discrimination against blacks in the Jim Crow South, and that one forgets that, say, the Jews and the Irish also suffered from pervasive discrimination. Of course they did, but to see it as being of a comparable level and nature to that of African Americans is ludicrous. On the other hand saying so about the Japanese and Chinese is arguable. However, arguable and comparable does not mean the same, and one could say that the differences were so large that it doesn't make sense to see the two as equivalent.

What characterizes the comparable genocides is systematic slaughter that either clearly aimed at total extermination (with at least a semi-credible effort to do so) or even if that aim wasn't clear it killed off at least a bare majority of the targeted group.  Thus regardless of whether or not Americans aimed to exterminate all Native Americans or simply aimed at ethnic cleansing, the result was that most Native Americans died. On the other hand, whatever the Nazis long term aims were, there was no policy of total extermination of Poles during WWII, but instead one of reducing them to a nation of slaves and the total death toll was on the order of ten percent.

In my opinion the best argument for the uniqueness of the extermination of the European Jews is its motivation, the methodology argument somehow strikes me as of minor importance. It was done on behalf of an ideology that didn't merely see them as subhuman, nor did it have practical aims such as getting territory. Rather it was carried out as the result of a metaphysical belief that a particular race was the mortal enemy of all mankind and that its extermination was necessary if humanity was to be saved. The best argument against its uniqueness is that regardless of motive, history has seen various examples of atrocities either aiming at or reaching close to total extermination and as a practical matter the details of the ideology that lies behind  such acts are secondary to what actually happened.