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Windows Server 2003 I have heard good things about, but until it is running on something powerful enough to beat Kasparov in chess it is not the best Server OS.
Best desktop, OS X or Linux w/Gnome I would say.
Best hobby OS, for sure Linux. SkyOS may be neat, but it doesn't quite to the range of things Linux does for free .
Best software package: vi (no not really I just wanted to start a vi/emacs war)