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Go to any site, and click the Questions button, then the FAQ tab:

(all sites have them, those are just the examples)

So, how are those questions chosen? By the number of duplicates? I don't think it's by the number of views, the Ask Ubuntu one has a few questions that have only about 100 views.

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up vote 9 down vote accepted

The tooltip on that page says:

Questions with the most links

It's not restricted to "closed as dup" links - any question from the same site that is mentioned (in the question, answers or comments) gets "Linked".

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