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     On what basis can you say that one subjective standard is any better than another subjective standard?
How, exactly, are the unbiased, non-preferential, and non-sentient natural mechanisms of evolution in any way subjective?

  You can study evolutionary theory, crunch the numbers, and conclude that the Nazi's agenda would have resulted in fewer, less 'healthy' homo sapiens over a certain time frame, but that in itself does not make what the Nazi's did 'wrong'.  What if we take into account the emotional satisfaction that a Nazi would have felt when he looked around and saw nothing but blond hair and blue eyes? How can you quantify or rule out emotional flourishing as part of the good of human flourishing?  Moreover, how can you make a judgement call on how emotional flourishing compares to physical flourishing?
Simply put:
The emotional satisfaction of a few thousand Nazis + The physical and emotional suffering of the millions of victims of Nazi genocide + Artificially tampering with human evolution = A Net Loss for humankind.

Technically speaking, this is just my opinion, so I'd be interested to learn your thoughts on how the above equation results in a Net Gain.

     Interestingly enough, I think that you seriously underestimate the resiliency of evolutionary mechanisms to produce genetic diversity; after all, how did we get all the genetic diversity that we currently see in homo sapiens to begin with?  The only way your argument regarding 'limiting the available gene pool' works is if you restrict the time frame available for nature to work.  In the long run there is no reason to think that nature cannot recover the loss of genetic material and even produce a result superior to what would have happened.  Isn't a 'severe limiting of the gene pool' exactly what has happened numerous times in the past through the mass extinctions?  Yet we seem to have more than enough genetic diversity today for nature to work with.
While you are probably correct that humans would ultimately continue to flourish post-Nazi eugenics program, it is a virtual certainty that (assuming the Nazi goal of world domination was achieved and their plans were implemented on a global scale) the systematic exclusion of a specific set of genes/traits would result in a weakened species.

For example:
Due to excessive poaching, the percentage of tuskless elephants http://sector9evolution.blogspot.com/2013/02/the-evolution-of-tuskless-elephants-due_22.html is skyrocketing. If such poaching continues, eventually (and very soon, biologically speaking) tusks will be a thing of the past. Until recently, tusks have been an evolutionary boon to elephants by providing for self-defense, foraging, and sexual posturing, but due to the unnatural influence of humans on the gene pool (inadvertent as it may be) a specific trait is being excluded in the reproductive process. Do you think the exclusion of tusks in the elephant population will result in a stronger species[1]?

BTW, I am unaware of any "mass extinction" of modern humans, at least any that are supported by legitimate scientific evidence (this means you, Noah's flood). Please enlighten us with some examples.
In the end, when we condemn the Nazi's for what they did I do not think that we are not doing so because of any analysis detailing the possible success or failure of their program in promoting human flourishing - we condemn them because what they attempted to do seems wrong, period.  And while I think that Median's vague proposal regarding morality fails and will continue to fail miserably no matter how much he attempts to bolster it, I think that most atheists and theists condemn the Nazi's due to similar considerations (e.g. the inherently warranted value of human dignity).  The only difference between an atheist and a theist is that the theist claims that while basing morality on human dignity is a coherent means of construing moral epistemology, it seems ultimately meaningless if not grounded in the existence of a supreme being.  So I think that atheists and theists for the most part will come to similar conclusions regarding what is right and wrong, but they will differ on what they feel is necessary to ground those conclusions.   
My post attempted to remove the Nazi moralistic question altogether by just addressing the evolutionary setback their programs would have provided mankind.

Can you explain why you consider morality meaningless without a god? One would think the benefits of limiting human suffering in the present would be self evident, but your take seems to be that we can't really know what will be most beneficial to mankind in the long run (even if it sometimes amounts to many thousands of years), so we shouldn't judge anything.

I guess you would side with Ozymandias while I'd be in Rorschach's corner[2], eh?
 1. Making them un-poachable does not make them any better suited to their day-to-day environment, BTW
 2. Google Watchmen if you have no idea what this means
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