I know that we have them on bottom, but it would be useful for me to have also on top, so that I don't need scroll down to switch between one site and another.
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We now sort the gen-u-wine sites list by the amount of reputation you have on each site.
You must have a minimum of 200 rep on any given site to have it appear in anything other than random order, though.
I think it would clutter the header with links that most people rarely need due to Bookmarks. That's not to say that I don't use the links at the bottom. I just don't see the need to put them on the top.