On the mechanics of the post itself: I like putting the footnotes off to the side of the body. The alternative - using hyperlinks to jump back and forth from the location tot he end - is more intrusive.
I think footnotes are an artifact of dead tree printing; that it has been translated directly to interactive media is ludicrous. I predict its extinction, but the wait is very surprising.
(Putting footnotes within the page itself causes the page to be wider, which could potentially make the article harder to read on mobile devices. But at this point, a Javascript "popup window" solution would probably be worse.)