In the late Neolithic/Copper Age/early Bronze Age period, in what is now southern Poland, the incoming Indo-European Corded War culture people, who were metal age farmers with horses, were executing women and children from the invaded existing (probably non-Indo-European) Globular Amphora culture of semi-nomadic cow and pig herders, and then burying them in mass graves.
Around 2,800 BCE, in what is now southern Poland, a family group of fifteen individuals associated with the Globular Amphora culture (GAC) were massacred. They were probably captured and executed, because each victim was killed with a blow to the head from the same type of weapon, possibly a stone axe, and lacked defensive wounds. The dead were mostly women and children. They were buried in a mass grave, but with great care and very likely by someone who knew them well.
This Late Neolithic mass grave is the focus of a new ancient DNA and archeological research paper at PNAS by Schroeder et al. (see here). The authors tentatively attribute the massacre to the Corded Ware culture (CWC) people, who were expanding rapidly at the time across much of Europe from their homeland on the Pontic-Caspian steppe.
UPDATE May 9, 2019:
Razib Khan has some detailed genetic analysis and interesting speculations about the likely context of the killings (he thinks that the slaughter may have occurred while the adult warrior men were away from the village and then lovingly and carefully buried the kin that they discovered when they returned, which is a historically attested tactic in pre-modern war).
The genocide that came to Poland later, during World War II, should be familiar to everyone, even though, in fact, many people never learned anything about it.
Bell Beaker blogger, meanwhile, recounts a group grave from Spain from the Bell Beaker era (basically, Copper Age/early Bronze Age) containing multiple girls who were beheaded, although this account has less context for why this might have been done.
In both cases, the massacres were from the prehistoric era. But, in my view, legendary historical Biblical accounts of the ancient Hebrews committing similar atrocities, for example, in Chapter 31 of the Hebrew Bible book of Numbers, provide the best attested insights from a period as close in time as we have available, about the kinds of political and social contexts that this could have involved.