They tend to come from outfits with a vested interest in pleasing the Microsoft or MS-reliant businesses. Some have a long history of web-metrics -- but their (software) tools and websites are intrinsically MS-centric/biased. The rest tend to measure by "sales" in dollars, rather than usage, (partly because this is really the only hard data they can get their hands on). This is like comparing taxi usage to walking.
Additionally, most systems come with Windows pre-installed, this default Windows OS gets scrubbed in favor of a Linux install -- so this Linux (or BSD) gets counted as Windows. And because of the licensing, one Linux CD can legally (and conveniently) be used to install a whole whack of boxes, which skews the number even more.
I've never heard of good, methodologically sound numbers anywhere. And it shouldn't matter anyways. The REAL QUESTION is; "Can it do what I need done, and how much work will be necessary if I do choose to switch over?"
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PS: But Linux is common in F500 companies, and I personally have run across its use in small, non-technical firms that don't even have an "IT" department (eg. an accounting/financial-advice firm, that converted its servers and 1/2 its desktops -- all install/admin by the accountants themselves).
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