[Ribs]

On the fall - The way it's done is very subtle at hiding things. Sherlock jumps off the building, Watson runs over and falls down, we see Sherlock's body land on the path (but at a different angle then he fell) and he has no pulse and blood is on his head. On Watson's blog (johnwatson.co.uk) there is no report of Moriarty/Brooks' body on the roof as well.

My theory on how it's done - there's a gap in time between Moriarty's death and John arriving. Sherlock then takes a small dosage of one of the chemicals mentioned earlier in the episode (which also featured in the Ritchie films) that also slows your pulse. This takes a few minutes to take effect, so he bides the time once John arrives by talking to him. A side effect of said chemical is watery eyes - thus explaining why Sherlock starts tearing up. Once he tears up, he's able to jump, and jumps. Molly/Mycroft hired someone to slow John down by knocking him over, and John fails to see Sherlock cushion his fall by landing in the nearby garbage truck, pouring blood Molly supplied to him on his face (the blood is clearly not coming from his head when watched at an angle). Sherlock then rolls out of the truck and lands with a few feet's fall onto the path, where he is surrounded by a group of people. Watson walks over and takes his pulse as the body is taken inside. Molly switches the body with that of Moriarty from the roof, and Mycroft 'confirms' that the body is Sherlock's, and Moriarty is buried in Sherlock's place.

My other favorite theory is that the building Sherlock is standing on is not the same building that Watson is seeing Sherlock fall from, and it is instead a double. Which'd be mad but brilliant.