Continuing the recent wave of anxiety (to put it lightly), the New York Times has an AP story about the General Accounting Office's opinion on the security of our nation's computers. According to the GAO, there are "pervasive" security weaknesses at the government's 24 largest departments and agencies (including the Department of Defense, whose need for secrecy should be obvious, and the Department of Energy, which oversees our nuclear program). Interestingly, the GAO points out that one major source of weakness is a lack of protection against insiders sabotaging systems or purloining information ("the disgruntled organization insider is a significant threat, since such individuals often have knowledge that allows them to gain unrestricted access and inflict damage or steal assets").
The AP article can be found here. The GAO's report to the House can be found here.
Although the report makes no mention of Windows vs. open-source software, I think it's worth mentioning that many countries have moved (or are planning to move) toward open-source as a way of increasing cybersecurity, including Japan and Taiwan.