Here's some statistical data regarding OS distribution on the top 500 supercomputers. Far and away Linux dominates at an 87.80% share, traditional Unix taking a distant second, with a negligible Windows presence at 1%.
By OS family:
http://www.top500.org/stats/list/32/osfam
By OS:
http://www.top500.org/stats/list/32/os
http://www.top500.org/charts/list/32/os (pretty pie-chart.)