Personally I go with Virgin because (a) it's easier to earn/keep my status and (b) I'm uncomfortable with the Qantas/Emirates tie-up and refuse to let my travel dollars prop up barbaric Middle Eastern theocracies. (I realise that VA is also in bed with EY but at least they provide the alternative SQ option.)

I don't think either airline is in any statistically significant sense more or less likely to crash, though I can understand preferring a 737 to a Fokker 50 if those are the options on your particular route.