In what is now a fairly old news story (but not old for me, as I was 'out of the loop,' as it were, and just found this news today), the Vatican office in charge of the website has switched to using Linux servers and Mac workstations.
They surely have a lot of work to do to get the Vatican Website up-to-date (it has been image-map-based and not very innovative, design-wise, for many years... but it is one of the oldest and most well-known websites in the world). But I know of a few other great sites maintained on Macs. This site would be included in that list ;-)