I just stuff mine. And here's why: If you fold it, over time the folds will create lines, lines create weak spots and weak spots could eventually lead to leaks in your fly. So, IMO, the best thing to do is stuff the fly into the stuff sack.
"If you play a Nicleback song backwards, you'll hear messages from the devil. Even worse, if you play it forward, you'll hear Nickleback." - Dave Grohl