Makes sense, as I doubt any super computer is being used in a "user friendly" fashion. Linux has long been the king of "Does work with little overhead" as long as you know how to tell it to do the work.
So in any area that is Math/computational heavy I would guess you would see tons of Linux.
However with distributed processing on the horizon in a very real way, the days of the "supercomputer" are most definitely limited. I believe I read somewhere that the worlds fastest super computer would have to churn for a month to equal the production from some of the top BOINC projects get everyday. I will have to go looking.
GE-Raven