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There is a nice how-to from Sander Temme about Ten Tips to Harden Your Website. There will be more on ApacheCon with the topic Hardening Enterprise Apache Installations Against Attacks

from the howto:

a well maintained, up-to-date Windows server may well be more secure than a stale, unmaintained Linux installation. Your task is to maintain and defend your website, not to engage in a religious war of one operating system versus another.

http://linuxgazette.net/180/temme.html