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Let's just all agree that Windows Server 2003 was the best server OS for the desktop.
My list would include Fedora Project for most interesting distribution development, GNOME Project for biggest Free Software usability improvements, Epiphany and Inkscape for most valuable forks, freedesktop.org xserver for most exciting technology preview, Enemy Territory for best Linux multiplayer game, Novel buying monkeys and chameleons in a box for most interesting acquisition and of course Mono for just kicking everything's arse. Oh yes and there was something funny involving SCO, but I already forgot what it was all about. :p