Patch practices. Here Windows shines (finally). With Windows Update being readily available and running by default as of XP SP2, things are finally looking up for Windows users. From the perspective of an end-user seeking to keep his computer up to date with the current vendor-supplied security patches, Windows sure does make things easy.
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Linux isnt too far in the distance, though. Most Linux distributions do a respectable job at automated security patch management. Many are opt-in, however, and the interface varies from one distribution to the next, making it a bit less easy to do things properly for a typical end-user.
The elapsed time from notification to patch, on the other hand, can vary substantially. Overall, and again from a highly subjective viewpoint, I give a slight edge to Linux, but I do feel that Microsoft has made great advances in the past few years.
Qualitative score: Windows gets an A- while Linux gets a B+.
With these scores in mind, I have absolutely no doubt that my data is safest on a Linux system than on a Windows system. And that ends my three-way comparison of the user-level security in OS X, Windows, and Linux. Ive tried to be as fair as I can, and have given credit where each is worthy of it and wrath where its not.
My overall winner remains Apples OS X, which offers the best of both worlds (UNIX and Windows-like) to me. I have the native desktop apps that I need to do business, and underneath it all is the familiar face of UNIX. Im at $HOME.
In closing, I should also say that a person determined to keep her data secure can certainly use any of these three operating systems successfully. Theres enough good in the worst of them (and bad in the best of them) that what matters most is really learning how to use all the security capabilities of the OS youre most comfortable with.