I'm curious about what posts does the Community user upvote... The description found while viewing it's user page is that it owns downvotes on spam/evil posts that get permanently deleted. It doesn't say anything about the upvotes... on what criteria does it upvote, and what posts?
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If you're referring to the 44405 votes to community user has cast (these are meta numbers), most of the downvotes (3021), I assume come for the reason explained in the Community user's profile "Own downvotes on spam/evil posts that get permanently deleted". But, there is no explanation for how or what its upvoting (on meta 41384). My guess is that the community user owns the votes on questions that are migrated to the site, when the account that originally cast the vote, does not have an associated vote on this site. This would explain why, until recently the SO community user didn't have any upvotes, and now doesn't have too many (231) and why the meta community user has so many upvotes, there were a lot of very popular questions migrated here, and I suspect a very small percentage of SO users have meta accounts.
I believe this means that when you upvote a CW question or answer, it's the Community user that owns the vote.