My theory is that Sherlock knew he would have to fake his own death, and he arranged with Molly that she would help by conducting the autopsy and confirming that the body was his. The fact that the death occurred at Barts would ensure that the body was taken into her lab. He told her that he needed her, but we didn't see what for - and isn't it likely that he needed her in her capacity as a forensic pathologist, rather than as a woman/individual?

I think that the body which fell off the roof was Moriarty's - Sherlock put his scarf and his trademark coat on Moriarty's body, held him up on the rooftop when he saw John return, and the distance combined with his phone call to John convinced John that he was seeing Sherlock on the roof, and that it was he whom he saw fall. Moriarty's face was destroyed by the bullet, so it was unrecognisable. Molly would say that the injuries resulted from the fall. We didn't get a clear shot of the face, and John was too upset by seeing him fall to look closely.

My niece's clever gloss on this theory is that Sherlock got hold of the Sherlock mask and wig which Moriarty must have used when he kidnapped the children (the girl "recognised" him), and he told Molly he'd use it and she must not reveal it. I'm not sure if Mycroft knows - I rather think he doesn't.

I do hope that the ending means that we will have more series, and as soon as possible.

(Off to check what everyone else thinks about the episode!)