The murder of one person is bad enough. They were both horrific but I'm going to have to go with the Uyghur Genocide, as it specifically targets and persecutes people for their religion.
Tbf the Indonesian killings do overlap with a racist wave of pogroms particularly targeted at Chinese Christians.
The Indonesian mass killings, come to think about it, actually have a lot of similarity to the Reign of Terror in France.
It's a complicated question. What you have in this case is a central government allowing gangs of nationalist and ultra religious groups In tandem with the army to run rampaging through the country settling local scores. Often, local Chinese communities were a very visible source of resentment (a lot of anti-Chinese sentiment in SE Asia is very reminiscent of the tropes of European Anti Semitism) and they would get swept up in the bloodshed, especially in Sumatra and Kalimantan.
Other targets were those Muslims following a Javanese syncretic sect, Abangan, who were far more loathed than the christians and Hindus. (Although there was a similar non-Islamic wave of violence in Bali, led by upper caste Hindus using the PKI repression to target the lower castes - essentially you have everybody using the legalization of killing people without trial to really go bloodletting)
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