A short, open access review paper by Isabel Alves and colleagues  registers two important points:
Until recently, the out-of-Africa model of human evolution was favoured by most genetic analyses, but this model collapsed when the sequencing of the Neanderthal genome revealed that 1%–3% of the genome of Eurasians was of Neanderthal origin. At the same time, refined analyses of modern human genomic data – have changed our view of evolutionary forces acting on our genome. While most people assumed that the out-of-Africa expansion had been characterized by a series of adaptations to new environments – leading to recurrent selective sweeps , our genome actually contains little trace of recent complete sweeps , ,  and the genetic differentiation of human population has been very progressive over time, probably without major adaptive episodes .
I disagree slightly with the latter point about selection -- in fact, we have abundant signs of recent positive selection in the genome, but those signs are nearly all very recent partial sweeps in different human populations. Complete sweeps and near-complete sweeps are indeed few, suggesting that there was relatively little directional adaptive evolution associated with the "origin of modern humans." Measuring by genetic change, agriculture was many times more important than the appearance of modern humans throughout the world. The important point with respect to archaic humans is that there are precious few genetic changes shared by all (or even most) humans today, that are not also shared with Neandertals, Denisovans, or plausible other archaic human groups (such as archaic Africans).
That of course follows from the fact that a fraction of today's gene pool actually comes from those ancient groups. Their variation is (by and large) human variation..
Most anthropologists do not yet fully understand this genetic picture. We cannot presently define "human" in a genetic sense without including Neandertals.
Alves and colleagues discuss some important corollaries of the two key observations above. An important one:
Even though our simulated scenario is unrealistically simple, it is likely that differential admixture should affect population genetic affinities under more complex models of population differentiation. The proper interpretation of human genetic affinities should thus probably be re-evaluated in the light of these results.
A lot of studies of human genetic variation have assumed no mixture with archaic humans. Such studies are now obsolete. Whole-genome evidence is coming online, and with that evidence we must apply new analytical methods that incorporate more complex demographic hypotheses. These more complex models will require greater attention from anthropologists and population geneticists, but they should give us a more accurate picture of the causes and background of human diversity.
- . Genomic Data Reveal a Complex Making of Humans . PLoS Genetics. 2012;8(7):e1002837.