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Linux lacks any clear-cut system for determining which is the most popular or the best distribution, or which desktop environment is used more than others. That may be one of the major frustrations among Linux developers trying to spread the word about adopting the Linux desktop instead of Microsoft Windows or Apple's OS X.
Linux, like the countless denominations of religions, is a product of technology, ideology and endless options. Unlike its competitors, the Linux OS is not sold. It just is available to those who know about it.
I think this difficulty in tracking Linux users really only matters if there is some active push to tip the power balance in the OS world.
I do not use Linux in hopes that someday it will unseat another operating system; rather, I use it because I have the freedom to manipulate my implementation of it to suit my needs. I do appreciate the fact that it is free software, but if efforts to displace Windows or OSX were to become serious, that would require dollars for marketing, mass distribution, and licensing. And with so many distributions to choose from, not many individual Linux developers would be able to raise enough capital to endorse their implementation above all of the others. This could lead to mergers of several different Linuxes, if you pardon the term, to strengthen fundraising efforts. One of the cornerstones of Linux is variety, a benefit which then might begin to fade.
In our connected world where most people use the Internet probably the best metric we could get would be which distros are accessing web sites. Ideally we could get those numbers for the most popular web sites and that would give a pretty good reflection on what is being used on the desktop. We do have those numbers from Wikimedia, which includes Wikipedia, the fifth most popular website:
I think that provides a really good indication of what platforms are being used in the real world. Sure, some users spoof their User Agent string, but I would guess that would be a statistally insignificant number that has an equal effect across desktops.
Obviously everyone doesn't use Wikipedia, and ideally we could get an even more accurate number if we could get similar statistics from Google and Yahoo.
Even so, I think these numbers are a lot closer to the true platform use than either download numbers or Distrowatch page-hits.