I'd say the choice is more down to what you want to do with the server. Everything you use has bugs, and running software on platforms differant from the main development platform is likely to produce far more problems than anything. So for example, the majority of php users run on linux servers, as do people using mysql. I would therefore never use windows for that platform. It will work, but is likely to be sub optimal and the majority of the information on the net tends to be about the most common platform.
In comparison, if I was to develop .net applications, I would choose a windows server. While it is possible to run .net on a linux server (with the appropriate apache modules) the full .net API is only partly working.
Also, your own skills and familiarity should be taken into account also. Choosing to run a linux server when you are not familiar with linux or Unix will likely be a very painful learning curve.
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