Steven Moffat, in an interview, mentioned that the clue to the fall was something rather uncharacteristic Sherlock did in the episode but something most people missed. For people who have read the books, his treatment of the reporter - when he says "You repel me" – is hardly like Sherlock. He's merely very blunt but factual – not mean on purpose. That was an opinion and Sherlock is far too indifferent to form personal opinions of people. And sure enough - lots of people think so. In fact, the idea most of them gather is that the word of relevance is "rappel". The basic idea is that Sherlock uses a bungee rope during the fall to decelerate him enough before impact such that he’s relatively unharmed and then poses as the body to deceive Watson.
We need to remember that Sherlock was prepared to feign a suicide and that the arrangements he made were in accordance with the idea that Moriarty himself would also need to be deceived, should it come to that. Because no matter how you slice it, the opinion that Sherlock could have foreseen Moriarty’s suicide holds no water.
So he uses a bungee attached to some part of the roof, but strictly not visible to anyone on the roof itself. In all likelihood, something attached just under the roof and positioned such that he could grab the same as soon as he falls. We need to be clear on the fact that the bungee is attachable and not held on to by him, because the visuals would contradict such an idea. When he’s close enough to the ground, i.e. out of Watson’s line of sight, he detaches the bungee and hits the ground. Needless to say, Sherlock would have ensured that given his weight, the bungee decelerates to a velocity low enough for him to hit the ground without sustaining significant damage.
Post impact, most things do not change from the original idea. The crowd around his body is essentially comprised of the Baker Street irregulars (the homeless network, to those unfamiliar with the books), the person knocking down Watson also being a part of the same. And by doing so, he gives Sherlock the time to get blood on his face and impersonate a dead body. Also, the fact that Watson isn’t allowed to properly take a pulse becomes especially noteworthy in that light. As for Molly, Sherlock requires her to possibly falsify DNA records to ensure his death is verified and/or to confirm the same – since she’s a mortician or coroner at St. Barts.
On to the interesting bit –proof! Slow down (.25x - 1:23:25 onwards) - the bit where the sniper aiming at Watson draws the pointer away and you notice as he scrolls up, a piece of rope/string near the ceiling. It's not conclusive but it is easily the most blatant clue in the episode if the theory holds!