"Once you have eliminated the impossible, whatever remains, however improbable, must be true."
I do not believe that a mask/plastic surgery was used, nor do I believe that it was Moriarty or another corpse who was on the ground or thrown. That just isn't 'Sherlock' imo.
We can clearly see that Sherlock was the one stood on the ledge and it is the same Sherlock who jumps. Moriarty was laid prone on the rooftop of St. Bart's. I'm of the suspicion that Moriarty remains alive somehow (no idea how, though). Like all great Heroes and Villains, Sherlock and Moriarty live for the existence of the other. Anyway, onto Sherlock......
1. Note that Watson did not see the impact of the fall ,as Sherlock begged him to stay where he was (Specifically: 'Keep your eyes fixed on me'). I suspect that Sherlock jumped into the rubbish truck which was immediately beside where he 'landed'. From a height of 60-odd feet, he would be travelling at 43mph as he hit the ground. That impact cannot be survivable on concrete. However a shorter fall onto a big heap of rubbish bags? Easily survivable. Also, Sherlock was laid at a different angle to that at which he was falling - almost perpendicular. Yet parallel to the truck, had he rolled off it.
2. It takes an age for Watson to reach the body, as he is disoriented by a collision with a cyclist. I suspect that the cyclist was one of Sherlock's Homeless Network employed to daze Watson. Sherlock could easily have landed in the rubbish truck and rolled to reposition himself on the ground. Similarly, I believe that the people who quickly surround Sherlock are also part of the Homeless Network; a ploy to further delay Watson reaching him.
3. Sherlock, earlier, had a 'moment' with Molly, the girl in the morgue who fancies him like mad. Sherlock tells Molly that she is very important to him, and it is evident that she'd do anything for him. She could easily supply some blood (real or otherwise) and then interfere with autopsy reports etc. It could even be that Molly was positioned below as Sherlock jumped, to supply this blood.
4. Watson feels for Sherlock's pulse, which doesn't seem to be there. HOW do you stop a pulse? Well, Sherlock was playing with a squash-ball earlier in the episode. If you place a squash-ball under the armpit, you can stop a pulse in the wrist from being felt. Another way of stopping the pulse would be the consumption of rhododendron (the flower found on the kidnapper's shoe, earlier in the episode - so Sherlock would've had some in his possession).
5. Mycroft's ambivalence to his brother's death suggests to me that he too (as well as Molly) was in on what Sherlock was planning (in spite of their fiery relationship). It was Mycroft that 'unwittingly' gave some of Sherlock's life secrets to Moriarty. This may have been part of the plan to convince Watson that Sherlock really was dead. Also, Mycroft could play a part in document forgery (with regards to the autopsy by Molly).
6. I believe that Watson HAD to believe Sherlock was dead in order that everyone else believe's it. Sherlock's closest companion is the one who 'would truly know' after all. Also, Sherlock knows Watson's 'human' mannerisms and would know that Watson would really believe that his friend was dead.
Sherlock is alive and I think the above provides a good explanation as to how he did it. HOWEVER.......other worthy notes:
- Watson keeping his eyes fixed on Sherlock meant he didn't see the moment of impact. This is the argument I use for 'landing in the truck and rolling onto the ground', but who's to say that Molly wasn't also waiting below with blood - having had previous instruction from Sherlock, along with the Homeless Network.
- The high-pitched noise we hear as Watson is disoriented is similar to the noise we hear regularly throughout the 'Hound of Baskervilles' episode; could his disorientation be caused by that same drug/fear stimulant? Perhaps the drug was issued somehow by the passing cyclist? The Sun blocking his eyes has the same blinding effect as when the lights were turned on in the lab in HoB, after taking that drug.
- The rubbish truck drives away after the body 'lands'. Is Sherlock on the ground? Or has he been carried off? The body on the ground could be PERCEIVED to be Sherlock by Watson if he'd taken that fear-stimulant drug. They saw the hound 'because they expected to see it'. Maybe Watson (and the audience) saw Sherlock's body in a similar way - expected to see him dead? I don't believe this is very 'Sherlock' but is perfectly possible and fairly simple.
- Sherlock asked Moriarty for 'privacy'......was this so that the 'Molly' set-up could occur without Moriarty's knowledge? Once set-up, Sherlock could turn to Moriarty with the 'as long as you're alive' story, knowing Moriarty would be insane enough to kill himself.
- 'Keep your eyes fixed on me' kept Watson standing where he was. Crucially, this may have restricted the view of the sniper too. Perhaps causing the sniper to only see Sherlock's fall and not the impact.
It's my opinion that Sherlock provoked Moriarty into this set-up, and pulled it off remarkably well.
EDIT! Some thoughts.
Steven Moffat and Mark Gatiss have stuck remarkably well to the book narrative. That suggests to me that Moriarty will somehow have fallen from the roof WITH Sherlock (unless it is metaphorical, given he's shot himself).
Also, before Sherlock reappears, Mycroft has Mrs Hudson rearrange a dummy of Sherlock 20/30 times a day in the window of 221B Baker St, in order to fool further enemies (Moriarty henchmen?).