There are many theories floating around at the minute and Den of Geeks has some of the best (and weirdest). Although Steven Moffat himself has read all of them and suggests that EVERYONE has missed one extremely important clue that is within the episode itself. He also says that Sherlock does something entirely unlike himself which may lead audiences to see said clue.
However Sherlock does alot in this episode that we could consider unlike him. His treatment of Molly, his reaction to Moriarty's death, his speech to John, the fact he rings him instead of texts ('I prefer to text')etc. So there is a lot we can take from that.
But to me these are the important facts to take in to account.
1) Sherlock's interaction with Molly, telling her 'counts'. Molly not only has access to the morgue but to the hospital supplies as well, scrubs, stethoscopes etc.
2) Sherlock making John watch him from a specific angle, there is a wall on the ground that blocks John's view of the pavement. Sherlock also makes him keep his eyes focused on him, we see Sherlock taking and moving on the ledge from the moment John arrives to when he jumps, there could be no substitute. Many suggest that it's Moriarty's body wearing a Sherlock mask (previously used to scare the children earlier in the episode) and the fact that the papers in the aftermath don't refer to finding Jim. But that theory takes to much effort to undertake under the eyes of the audience and John.
3) The cyclist. After Sherlock falls, a cyclist knocks John over and disorientates him for precious few seconds. Does he have a concussion which affects his observations after? Is it really Sherlock he see's on the pavement. Why didn't the cyclist stop? surely if someone jumps off a building right next to you, you just don't carry on. IS he a well placed delay tactic because John was still on the other side of the wall and could not see Sherlock until he walked around it.
4) The Truck. There is a truck parked right next to the scene where Sherlock falls and the back door is open. After Sherlock falls the truck casually moves away, like the cyclist not paying attention to Sherlock or the people around. The truck is filled with rubbish or laundry and is open top. Could Sherlock have jumped in to the truck, then hopped out, popped a blood cap and act dead? or does the truck carry him away and the body left is one Molly was able to secure from the morgue that looked a bit like Sherlock?
5) The pulse. John takes Sherlocks pulse and is distraught when he feels nothing and his hand falls. Many suggest that the body is indeed either a well made fake or another person who is disguised to look like or resembles Sherlock. Whilst in the morgue beforehand however Sherlock is seen playing with a rubber ball casually as he makes John run on a wild goose chase to get him away from the scene. It is a scientifically proven fact that if you place a ball (tennis ball rubber ball etc) under your armpit and hold it firmly then it can stop the ability to feel the pulse in the wrist. John does not check Sherlock's neck pulse because he lapses in to shock, so this could be an explanation for that.
6) The people around the scene. There is an abundance of people surrounding the hospital as you would expect. Patients, Doctors on break, paramedics etc. All seem to rush to the scene quickly again as you would expect. But they could be well timed placements. I have previously suggested that Molly has access to a variety of items such as scrubs and uniforms, so the people may not be staff at all but people from The Baker Street Irregulars such as the Homeless Network brought in to convey Sherlock's 'body' away from the scene. It happens extremely quickly the movement and apart from John no one seems to check if Sherlock has a pulse. Very suspicious.
These are just some of the things I noticed in the episode, as I am a film student i try very hard to pay attention and the excellent writing and direction of the episode has me baffled for explanations. These points can be found in many theories online too
