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Typically, when something is listed as the Best of the year, it's because it debuted or made some kind of major milesone during that year. Though Linux, FreeBSD, and Solaris are all great server OSes, none of them had the kind of major release (as far as an increase in quality or capability) as Windows 2003 Server did. Linux probably has deserved the "best server OS" prize a few times over the past few years for its accomplishments.
Whenever Time's person of the year ends up being a bad guy (Hitler was man of the year one year) it always causes the same controversy. Sometimes the product or person with the biggest impact isn't the one you want to succeed, but the impact is there nonetheless.