I haven't read all of this thread, but I can see some clarifications would be useful.
First, I would suggest that 'altruism' be reserved to refer to behavior that benefits another *of the same species* at a (potential) cost to the actor. (We can forget about inter-species acts of altruism because they can't be selected for within a population - even if they do occasionally occur).
Second, (not sure if anyone else has pointed this out yet) your assumption regarding the general degree of genetic relatedness among all humans cannot be extrapolated to a 'Kin Selection' argument for larger unrelated groups. That is because your 99.9 % genetic similarity has a quantitative derivation from DNA sequence homology estimates - it does not translate directly to qualitative differences in actual genes or any specific units of selection. With just 0.1% differences carefully placed on the genome you could create a very large number of functional gene differences - you could easily end up with extremely divergent genotypes.
One author who is worth reading on this subject is
Richard Alexander.
He has put forward the idea that, in human societies at least, altruism has evolved under group selection as an extension of kin selection. In brief, selfless behaviors that evolved because of advantages conferred through inclusive fitness were natural precursors for altruistic behaviors toward unrelated individuals of the same species. The advantages of such costly, selfless behaviors become readily evident in larger groups and organized societies, and some of them turn out to be a lot less 'selfless' than they seem on the surface. For example, the direct individual benefits and recognitions conferred by society at large on the guy that runs into a buring house to save a baby.
But back to group selection and why it is so important to evolution of altruism. As extended family groups became larger and competed with one another for territory and resources, the spoils of inter-group conflicts often went to the larger groups. Groups that were able to cooperate well with unrelated individuals and integrate them had competitive advantages in inter-group conflict. Thus, ironically, human group conflict was likely one of the strongest evolutionary forces selecting for altruistic behavior toward unrelated individuals. Most altruistic behaviors are really rooted in the selfish interests of individual selection - whether that is readily apparent in their execution or not.
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