Or is everything saved in a cookie? I am aware that unregistered users are tracked by their cookies, but I think SO needs some reference to the owner of the question, and thus they must store some data?
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Unregistered users are essentially the same as registered users; the only big difference is their OpenID is a randomly generated GUID:
If they do decide to "register" the GUID is replaced with their actual OpenID, which will let them login in the future
Yes, of course.. Also because when they register they have all their old posts assigned to their account, so at the very least they have to save enough data to do that.